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INTRODUCTION

Protein Data Bank Exchange macromolecular Crystallographic Information Framework, PDBx/mmCIF, provides the foundation for the deposition, annotation, and archiving of structural data across various experimental techniques.

PDBx/mmCIF uses data blocks to organize related information and data. A data block is a logical partition of a data file designated by a data_ record. A data block may be named by appending a text string after the data_ record and a data block is terminated by either another data_ record or by the end of the file.

An example of identifying data block at the beginning of the model file for the PDB entry 4HHB:

data_4HHB
#
_entry.id4HHB
#
_audit_conform.dict_namemmcif_pdbx.dic
_audit_conform.dict_version5.367
_audit_conform.dict_locationhttp://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#

PDBx/mmCIF format utilizes the ASCII character set. All data items are identified by name, begin with the underscore character, and are composed of a category name followed by an attribute name. The category name is separated from the attribute name by a period.

An example of PDBx/mmCIF data item (_category.attribute):

_entity.id

Data items are presented in two styles: key-value and tabular.

An example of a key-value style where the PDBx/mmCIF item is followed directly by a corresponding value:

_cell.entry_id4HHB
_cell.length_a63.150
_cell.length_b83.590
_cell.length_c53.800
_cell.angle_alpha90.00
_cell.angle_beta99.34
_cell.angle_gamma90.00
_cell.Z_PDB4

An example of a tabular style used when there are multiple values for each item. In this style, a loop_ record is followed by rows of data item names and then white-space delimited data values:

loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Fermi, G.' 1 0000-000x-xxxx-xxxx
'Perutz, M.F' 2 0000-000x-xxxx-xxxx

The hash symbol (#) is used to separate categories to improve readability, but is not strictly necessary. It is also used to indicate comments.

Numbers and single-word data values (i.e., those not containing white space) are listed by themselves:

_cell.length_a 63.150

A single value composed of multiple words separated by white-space need to be quoted:

_audit_author.name 'Fermi, G.'

A single value encompassing multiple line data values can be listed on a new line within a pair of semicolons:

loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_target_identifier
1 'polypeptide (L)' no no
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
A,C ?

There are two special characters used as placeholders for mmCIF item values which for some reason cannot be explicitly assigned. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.

The PDBx/mmCIF Dictionary supports primary data types (integers, real numbers, and text), defines boundary conditions and controlled vocabularies, and provides the ability to link data items together to express relationships (e.g., parent-child related data items).

For example, the entity identifier assigned to a molecule in the "parent" _entity data category (shown here) is referred to in the "child" categories (as shown in the subsequent example):

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer nat 'Hemoglobin subunit alpha' 14981.087 1 ? ? ? ?
2 polymer nat 'Hemoglobin subunit beta' 16032.274 1 ? ? ? ?
3 non-polymer syn 'PROTOPORPHYRIN IX CONTAINING FE' 616.487 2 ? ? ? ?
4 water nat water 18.015 93 ? ? ? ?

Example of a "child" category describing the source information for each polymer entity listed in the above "parent" category:

loop_
_entity_src_nat.entity_id
_entity_src_nat.pdbx_src_id
_entity_src_nat.pdbx_alt_source_flag
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seq_num
_entity_src_nat.common_name
_entity_src_nat.pdbx_organism_scientific
_entity_src_nat.pdbx_ncbi_taxonomy_id
1 1 sample 1 140 horse 'Equus caballus' 9796
2 1 sample 1 146 horse 'Equus caballus' 9796

The primary PDBx/mmCIF resource mmcif.wwpdb.org contains all relevant data dictionaries and documentation, as well as a detailed description of the format's development and history. The below sections present some key PDBx/mmCIF categories with descriptions and examples, and aim to help users to understand and adopt the PDBx/mmCIF format.

HEADER AND KEYWORDS

PDBx/mmCIF category Legacy PDB format records Description
_struct_keywords HEADER KEYWDS Keywords that describe the structure.

Example:

_struct_keywords.entry_id 8HRI
_struct_keywords.text 'SARS-CoV-2, Delta, Spike protein, VIRAL PROTEIN'
_struct_keywords.pdbx_keywords 'VIRAL PROTEIN'

TITLE AND AUTHORSHIP

PDBx/mmCIF category Legacy PDB format records Description
_struct TITLE Structure title.

Example:

_struct.entry_id 8HYP
_struct.title 'Crystal structure of AtHPPD-Y18400 complex'
PDBx/mmCIF category Legacy PDB format records Description
_audit_author AUTHOR Structure author(s).

Example:

loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Fermi, G.' 1 ?
'Perutz, M.F.' 2 ?

CITATION

PDBx/mmCIF category Legacy PDB format record Description
_citation JRNL Literature citations relevant to the contents of the entry.

Notes:

  • The _citation.id 'primary' is used for the citation describing structure determination and refinement.
  • The corresponding authors for each citation are listed in the 'child' _citation_author category (see below).

Example:

loop_
_citation.id
_citation.title
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.country
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_publisher
_citation.pdbx_database_id_PubMed
_citation.pdbx_database_id_DOI
primary 'Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor.' Nat.Struct.Biol. 8 874 878 2001 NSBIEW US 1072-8368 2024 ? 11573093 10.1038/nsb1001-874
1 'ISOLATION OF A COMMON RECEPTOR FOR COXSACKIE B VIRUSES AND ADENOVIRUSES 2 AND 5' Science 275 1320 1323 1997 SCIEAS US 0036-8075 0038 ? ? 10.1126/science.275.5304.1320
PDBx/mmCIF category Legacy PDB format records Description
_citation_author JRNL Citation author(s).

Notes:

  • The value in _citation_author.citation_id item points to the relevant citation information in the 'parent' _citation category (see above) linking citations with the corresponding authors.

Example:

loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'He, Y.' 1 ?
primary 'Chipman, P.R.' 2 ?
primary 'Howitt, J.' 3 ?
primary 'Bator, C.M.' 4 ?
primary 'Whitt, M.A.' 5 ?
primary 'Baker, T.S.' 6 ?
primary 'Kuhn, R.J.' 7 ?
primary 'Anderson, C.W.' 8 ?
primary 'Freimuth, P.' 9 ?
primary 'Rossman, M.G.' 10 ?
1 'Bergelson, J.M.' 11 ?
1 'Cunningham, J.A.' 12 ?
1 'Droguett, G.' 13 ?
1 'Kurt-Jones, E.A.' 14 ?
1 'Krithivas, A.' 15 ?
1 'Hong, J.S.' 16 ?
1 'Horwitz, M.S.' 17 ?
1 'Crowell, R.L.' 18 ?
1 'Finberg, R.W.' 19 ?

EXPERIMENTAL METHOD

PDBx/mmCIF category Legacy PDB format records Description
_exptl EXPDTA Experimental method used to collect data.

Example:

_exptl.entry_id 4HHB
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number ?

Example:

loop_
_exptl.entry_id
_exptl.crystals_number
_exptl.details
_exptl.method
_exptl.method_details
8W48 1 ? 'X-RAY DIFFRACTION' ?
8W48 ? ? 'NEUTRON DIFFRACTION' ?

MACROMOLECULES

Entry Composition and Details

PDBx/mmCIF category Legacy PDB format records Description
_entity COMPND Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.

Notes:

  • _entity.id is a unique identifier of all unique polymer and non-polymer molecules in the structure. This value is referred to in many 'child' categories within the model file connecting all the information pertaining to a particular molecular entity together.
  • _entity.type can be: polymer, branched, non-polymer, or water.
  • Each polymer entity is expected to have a corresponding record in the _entity_poly, _entity_poly_seq, and _pdbx_poly_seq_scheme categories.
  • _entity.src_method - defines the type of method by which the entity was produced: naturally obtained (nat), recombinantly expressed (man), or chemically synthesized (syn).
  • Source information for each polymer entity must be provided in either _entity_src_nat (naturally obtained), _entity_src_gen (recombinantly expressed), or _pdbx_entity_src_syn (chemically synthesized).

Example:

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
1 polymer man 'Secreted effector kinase SteC' 19731.074 4 2.7.-.- C276S
2 non-polymer nat 'ADENOSINE MONOPHOSPHATE' 347.221 4 ? ?
3 non-polymer syn 'MAGNESIUM ION' 24.305 5 ? ?
4 water nat water 18.015 167 ? ?

Source and Expression System

PDBx/mmCIF category Legacy PDB format records Description
_entity_src_gen SOURCE Details of the source from which the entity was obtained in cases where the source was genetically manipulated, including the organism from which the gene was obtained and the host organism for gene expression and details about the host organism (e.g., the plasmid used).

Notes:

Example:

_entity_src_gen.entity_id 1
_entity_src_gen.pdbx_src_id 1
_entity_src_gen.pdbx_alt_source_flag sample
_entity_src_gen.pdbx_seq_type 'Biological sequence'
_entity_src_gen.pdbx_beg_seq_num 1
_entity_src_gen.pdbx_end_seq_num 299
_entity_src_gen.pdbx_gene_src_scientific_name 'Severe acute respiratory syndrome coronavirus 2'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2697049
_entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21 (DE3)'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008
PDBx/mmCIF category Legacy PDB format records Description
_entity_src_nat SOURCE Details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural source.

Example:

_entity_src_nat 1
_entity_src_nat.pdbx_src_id 1
_entity_src_nat.pdbx_alt_source_flag sample
_entity_src_nat.pdbx_beg_seq_num 1
_entity_src_nat.pdbx_end_seqe_num 129
_entity_src_nat.common_name chicken
_entity_src_nat.pdbx_organism_scientific 'Gallus gallus'
_entity_src_nat.pdbx_ncbi_taxonomy_id 9031
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_entity_src_syn SOURCE Details of the source from which the entity was obtained in cases where the entity was chemically synthesized.

Example:

_pdbx_entity_src_syn.entity_id 2
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num 1
_pdbx_entity_src_syn.pdbx_end_seq_num 64
_pdbx_entity_src_syn.organism_scientific 'Mandarin fish ranavirus'
_pdbx_entity_src_syn.ncbi_taxonomy_id 2487147

Sample Sequence

PDBx/mmCIF category Legacy PDB format records Description
_entity_poly SEQRES Details about the polymer, such as polymer type, corresponding chain IDs and studied polymer sequence.

Notes:

  • _entity_poly.pdbx_seq_one_letter_code describes the sequence of protein or nucleic acid polymers in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymers, each residue is represented by the code of its individual type. A cyclic polymer is represented in linear sequence from the chosen start to end.
  • _entity_poly.pdbx_seq_one_letter_code_can describes the canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in _entity_poly.pdbx_seq_one_letter_code. Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if parent is not specified. Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. For modifications with several parent amino acids, all corresponding parent amino acid codes will be listed (ex. chromophores).

Example:

loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_target_identifier
1 'polypeptide (L)' no no
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
;VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
;
A,C ?
2 'polypeptide (L)' no no
;VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
;
;VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
;
B,D ?
PDBx/mmCIF category Legacy PDB format records Description
_entity_poly_seq SEQRES Specifies the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.

Notes:

  • _entity_poly_seq.hetero defines a flag to indicate whether this monomer in the polymer is heterogeneous in sequence.

Example:

loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 VAL n
1 2 LEU n
1 3 SER n
1 4 PRO n
1 5 ALA n
1 6 ASP n
... (truncated for brevity)
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_poly_seq_scheme N/A Residue level nomenclature mapping for polymer entities.

Notes:

Example:

loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 VAL 1 1 1 VAL VAL A . n
A 1 2 LEU 2 2 2 LEU LEU A . n
A 1 3 SER 3 3 3 SER SER A . n
A 1 4 PRO 4 4 4 PRO PRO A . n
A 1 5 ALA 5 5 5 ALA ALA A . n
A 1 6 ASP 6 6 6 ASP ASP A . n
A 1 7 LYS 7 7 7 LYS LYS A . n
A 1 8 THR 8 8 8 THR THR A . n
A 1 9 ASN 9 9 9 ASN ASN A . n
A 1 10 VAL 10 10 10 VAL VAL A . n
A 1 11 LYS 11 11 11 LYS LYS A . n
A 1 12 ALA 12 12 12 ALA ALA A . n
A 1 13 ALA 13 13 13 ALA ALA A . n
A 1 14 TRP 14 14 14 TRP TRP A . n
A 1 15 GLY 15 15 15 GLY GLY A . n
A 1 16 LYS 16 16 16 LYS LYS A . n
A 1 17 VAL 17 17 17 VAL VAL A . n
A 1 18 GLY 18 18 18 GLY GLY A . n
A 1 19 ALA 19 19 19 ALA ALA A . n
... (truncated for brevity)
PDBx/mmCIF category Legacy PDB format records Description
_struct_asym N/A Details about instances of molecular entities.

Notes:

  • The category provides correspondence between molecule ASYM_ID (_struct_asym.id, a unique identifier of each molecule in the model) and corresponding Entity ID (_entity.id).
  • ASYM_ID can be different from the author provided or PDB assigned chain identifier (chain ID), ASYM_ID is assigned sequentially starting from letter A to all polymer and non-polymer molecule instances in the structure.
  • A group of water molecules associated with the same polymer chain is assigned one ASYM_ID.

Example:

loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 1 ?
C N N 1 ?
D N N 1 ?
E N N 2 ?
F N N 2 ?
G N N 2 ?
H N N 2 ?

Sequence Reference

PDBx/mmCIF category Legacy PDB format records Description
_struct_ref DBREF Relates the sequence of the polymer entities described in the structure to the information archived in external sequence databases (UniProt, GeneBank, PDB, etc.).

Notes:

  • _struct_ref.pdbx_seq_one_letter_code provides an external database sequence expressed as a string of one-letter amino acid codes. If no external database reference is provided, the PDB entry itself is used as a database reference (self-reference) in which case the studied sample sequence is provided here.

Example:

_struct_ref.id 1
_struct_ref.db_name UNP
_struct_ref.db_code Q93D82_RHIRD
_struct_ref.pdbx_db_accession Q93D82
_struct_ref.pdbx_db_isoform ?
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code
;TAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIF APEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKE LGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGG FPMIERWPGMPE
;
_struct_ref.pdbx_align_begin 3
PDBx/mmCIF category Legacy PDB format records Description
_struct_ref_seq DBREF Provides the residue ranges used for the alignment between the sequence of an entity described in the structure and the sequence in the referenced database entry.

Example:

loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 5KWE A 20 ? 271 ? Q93D82 3 ? 254 ? 3 254
2 1 5KWE B 20 ? 271 ? Q93D82 3 ? 254 ? 3 254
3 1 5KWE C 20 ? 271 ? Q93D82 3 ? 254 ? 3 254
4 1 5KWE D 20 ? 271 ? Q93D82 3 ? 254 ? 3 254
PDBx/mmCIF category Legacy PDB format records Description
_struct_ref_seq_dif SEQADV Lists differences (if any) between the sequence of the polymer entity described in the structure and the sequence of the referenced database entry with corresponding annotation (conflict, engineered mutation, variant, expression tag, etc.).

Example:

loop_
_struct_ref_seq_dif.align_id
_struct_ref_seq_dif.pdbx_pdb_id_code
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.pdbx_pdb_strand_id
_struct_ref_seq_dif.seq_num
_struct_ref_seq_dif.pdbx_pdb_ins_code
_struct_ref_seq_dif.pdbx_seq_db_name
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_ref_seq_dif.db_mon_id
_struct_ref_seq_dif.pdbx_seq_db_seq_num
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_auth_seq_num
_struct_ref_seq_dif.pdbx_ordinal
1 5KWE MET A 1 ? UNP Q93D82 ? ? 'initiating methionine' -16 1
1 5KWE GLY A 2 ? UNP Q93D82 ? ? 'expression tag' -15 2
1 5KWE HIS A 3 ? UNP Q93D82 ? ? 'expression tag' -14 3
1 5KWE HIS A 4 ? UNP Q93D82 ? ? 'expression tag' -13 4
1 5KWE HIS A 5 ? UNP Q93D82 ? ? 'expression tag' -12 5
1 5KWE HIS A 6 ? UNP Q93D82 ? ? 'expression tag' -11 6
1 5KWE HIS A 7 ? UNP Q93D82 ? ? 'expression tag' -10 7
1 5KWE HIS A 8 ? UNP Q93D82 ? ? 'expression tag' -9 8
1 5KWE SER A 9 ? UNP Q93D82 ? ? 'expression tag' -8 9
1 5KWE SER A 10 ? UNP Q93D82 ? ? 'expression tag' -7 10
1 5KWE GLY A 11 ? UNP Q93D82 ? ? 'expression tag' -6 11
1 5KWE LEU A 12 ? UNP Q93D82 ? ? 'expression tag' -5 12
1 5KWE VAL A 13 ? UNP Q93D82 ? ? 'expression tag' -4 13
1 5KWE PRO A 14 ? UNP Q93D82 ? ? 'expression tag' -3 14
1 5KWE ARG A 15 ? UNP Q93D82 ? ? 'expression tag' -2 15
1 5KWE GLY A 16 ? UNP Q93D82 ? ? 'expression tag' -1 16
1 5KWE SER A 17 ? UNP Q93D82 ? ? 'expression tag' 0 17
1 5KWE HIS A 18 ? UNP Q93D82 ? ? 'expression tag' 1 18
1 5KWE ALA A 19 ? UNP Q93D82 ? ? 'expression tag' 2 19
1 5KWE ASN A 170 ? UNP Q93D82 CYS 153 'engineered mutation' 153 20

OLIGOSACCHARIDES

Entry Composition and Details

PDBx/mmCIF category Legacy PDB format records Description
_entity COMPND Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.

Example:

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer man 'FUCOLECTIN-RELATED PROTEIN' 66769.758 1 ? YES 'CATALYTIC MODULE, RESIDUES 31-589' ?
2 branched man "alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose" 681.7 1 ? ? ? ?
3 water nat water 18.015 334 ? ? ? ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_entity_branch N/A Specifies the list of branched entities and the type.

Example:

_pdbx_entity_branch.entity_id 2
_pdbx_entity_branch.type oligosaccharide
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_entity_branch_descriptor N/A Provides string descriptors of entity chemical structure.

Example:

loop_
_pdbx_entity_branch_descriptor.ordinal
_pdbx_entity_branch_descriptor.entity_id
_pdbx_entity_branch_descriptor.descriptor
_pdbx_entity_branch_descriptor.type
_pdbx_entity_branch_descriptor.program
_pdbx_entity_branch_descriptor.program_version
1 2 "LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROH" "Glycam Condensed Sequence" GMML 1.0
2 2 "WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1" WURCS PDB2Glycan 1.1
3 2 "[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}" LINUCS PDB-CARE ?

Sequence

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_entity_branch_list N/A Specifies the list of monomers in a branched entity. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID.

Example:

loop_
_pdbx_entity_branch_list.entity_id
_pdbx_entity_branch_list.comp_id
_pdbx_entity_branch_list.num
_pdbx_entity_branch_list.hetero
2 NAG 1 n
2 GAL 2 n
2 FUC 3 n
2 FUC 4 n
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_branch_scheme N/A Residue level nomenclature mapping for branch chain entities.

Example:

loop_
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_mon_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.hetero
B 2 NAG 1 B NAG 1 A NAG 1592 n
B 2 GAL 2 B GAL 2 A GAL 1591 n
B 2 FUC 3 B FUC 3 A FUC 1590 n
B 2 FUC 4 B FUC 4 A FUC 1593 n

Connectivity

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_entity_branch_link N/A Details about the linkages between components within a branched entity.

Example:

loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
_pdbx_entity_branch_link.details
1 2 2 GAL C1 O1 1 NAG O4 HO4 sing ? ? ?
2 2 3 FUC C1 O1 2 GAL O2 HO2 sing ? ? ?
3 2 4 FUC C1 O1 1 NAG O3 HO3 sing ? ? ?
PDBx/mmCIF category Legacy PDB format records Description
_struct_conn
  • LINK
  • SSBOND
Details about the connections between portions of the structure. These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on.

Example:

loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1 covale one ? A ASN 91 ND2 ? ? ? 1_555 L NAG . C1 ? ? B ASN 91 B NAG 409 1_555 ? ? ? ? ? ? ? 1.440 ? N-Glycosylation
covale2 covale one ? A ASN 207 ND2 ? ? ? 1_555 C NAG . C1 ? ? B ASN 207 C NAG 1 1_555 ? ? ? ? ? ? ? 1.418 ? N-Glycosylation
covale3 covale one ? A ASN 305 ND2 ? ? ? 1_555 B NAG . C1 ? ? B ASN 305 A NAG 1 1_555 ? ? ? ? ? ? ? 1.451 ? N-Glycosylation
covale4 covale both ? B NAG . O4 ? ? ? 1_555 B NAG . C1 ? ? A NAG 1 A NAG 2 1_555 ? ? ? ? ? ? ? 1.357 ? ?
covale5 covale both ? C NAG . O4 ? ? ? 1_555 C NAG . C1 ? ? C NAG 1 C NAG 2 1_555 ? ? ? ? ? ? ? 1.369 ? ?
covale6 covale both ? C NAG . O4 ? ? ? 1_555 C BMA . C1 ? ? C NAG 2 C BMA 3 1_555 ? ? ? ? ? ? ? 1.374 ? ?
covale7 covale both ? C BMA . O6 ? ? ? 1_555 C MAN . C1 ? ? C BMA 3 C MAN 4 1_555 ? ? ? ? ? ? ? 1.363 ? ?
covale8 covale both ? C BMA . O3 ? ? ? 1_555 C MAN . C1 ? ? C BMA 3 C MAN 6 1_555 ? ? ? ? ? ? ? 1.353 ? ?
covale9 covale both ? C MAN . O3 ? ? ? 1_555 C MAN . C1 ? ? C MAN 4 C MAN 5 1_555 ? ? ? ? ? ? ? 1.346 ? ?

LIGANDS

Entry composition & details

PDBx/mmCIF category Legacy PDB format records Description
_entity COMPOUND Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure.

Example:

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer man '3C-like proteinase' 33825.547 1 3.4.22.69 ? ? ?
2 non-polymer syn
;(1R,2S,5S)-N-{(1E,2S)-1-imino-3[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
;
501.542 1 ? ? ? ?
3 water nat water 18.015 83 ? ? ? ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_entity_nonpoly N/A Provides mapping between entity and the non polymer component.

Example:

loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2
;(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
;
4WI
3 water HOH
PDBx/mmCIF category Legacy PDB format records Description
_chem_comp
  • HET
  • HETNAM
  • HETSYN
  • FORMUL
Details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, synonym, mass, or formula.

Example:

loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
4WI non-polymer .
;(1R,2S,5S)-N{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-
3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
;
'PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form' 'C23 H34 F3
N5 O4' 501.542
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093
ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103
... (truncated for brevity)
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nonpoly_scheme N/A Residue level nomenclature mapping for non-polymer entities.

Example:

loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 4WI 1 401 1 4WI UNL A .
C 3 HOH 1 501 12 HOH HOH A .
C 3 HOH 2 502 85 HOH HOH A .
C 3 HOH 3 503 52 HOH HOH A .
C 3 HOH 4 504 27 HOH HOH A .
C 3 HOH 5 505 29 HOH HOH A .
C 3 HOH 6 506 3 HOH HOH A .
C 3 HOH 7 507 23 HOH HOH A .
C 3 HOH 8 508 55 HOH HOH A .
C 3 HOH 9 509 42 HOH HOH A .
C 3 HOH 10 510 53 HOH HOH A .
... (truncated for brevity)

Connectivity

PDBx/mmCIF category Legacy PDB format records Description
_struct_conn LINK Details about the connections between portions of the structure. These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on.

Example:

_struct_conn.id covale1
_struct_conn.conn_type_id covale
_struct_conn.pdbx_leaving_atom_flag none
_struct_conn.pdbx_PDB_id ?
_struct_conn.ptnr1_label_asym_id A
_struct_conn.ptnr1_label_comp_id CYS
_struct_conn.ptnr1_label_seq_id 145
_struct_conn.ptnr1_label_atom_id SG
_struct_conn.pdbx_ptnr1_label_alt_id ?
_struct_conn.pdbx_ptnr1_PDB_ins_code ?
_struct_conn.pdbx_ptnr1_standard_comp_id ?
_struct_conn.ptnr1_symmetry 1_555
_struct_conn.ptnr2_label_asym_id B
_struct_conn.ptnr2_label_comp_id 4WI
_struct_conn.ptnr2_label_seq_id .
_struct_conn.ptnr2_label_atom_id C3
_struct_conn.pdbx_ptnr2_label_alt_id ?
_struct_conn.pdbx_ptnr2_PDB_ins_code ?
_struct_conn.ptnr1_auth_asym_id A
_struct_conn.ptnr1_auth_comp_id CYS
_struct_conn.ptnr1_auth_seq_id 145
_struct_conn.ptnr2_auth_asym_id A
_struct_conn.ptnr2_auth_comp_id 4WI
_struct_conn.ptnr2_auth_seq_id 401
_struct_conn.ptnr2_symmetry 1_555
_struct_conn.pdbx_ptnr3_label_atom_id ?
_struct_conn.pdbx_ptnr3_label_seq_id ?
_struct_conn.pdbx_ptnr3_label_comp_id ?
_struct_conn.pdbx_ptnr3_label_asym_id ?
_struct_conn.pdbx_ptnr3_label_alt_id ?
_struct_conn.pdbx_ptnr3_PDB_ins_code ?
_struct_conn.details ?
_struct_conn.pdbx_dist_value 1.804
_struct_conn.pdbx_value_order ?
_struct_conn.pdbx_role ?
PDBx/mmCIF category Legacy PDB format records Description
_chem_comp_bond N/A Details about the bonds and bond orders between atoms in a chemical component.

Example:

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
4WI O1 C8 doub N N 1
4WI C8 N2 sing N N 2
4WI C8 C5 sing N N 3
4WI N2 C7 sing N N 4
4WI C4 C5 sing N N 5
4WI C4 C2 sing N N 6
4WI C5 C6 sing N N 7
4WI N5 C3 doub N N 8
4WI C3 C2 sing N N 9
4WI C7 C6 sing N N 10
4WI C2 N1 sing N N 11
4WI N2 H9 sing N N 69
... (truncated for brevity)
PDBx/mmCIF category Legacy PDB format records Description
_chem_comp_atom N/A Details about the atoms in a chemical component.

Example:

loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
4WI C8 C N N 1
4WI C3 C N N 2
4WI C1 C N N 3
4WI C13 C N N 4
4WI C21 C N N 5
4WI C6 C N N 6
4WI C7 C N N 7
4WI C10 C N N 8
4WI C5 C N S 9
4WI C9 C N S 10
4WI C11 C N S 11
... (truncated for brevity)

Information Specific To Macromolecular Crystallography (MX)

Sample preparation

PDBx/mmCIF category Legacy PDB format records Description
_exptl_crystal_grow REMARK 280 Details about the conditions and methods used to grow the crystal.

Example:

_exptl_crystal_grow.apparatus ?
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP'
_exptl_crystal_grow.pH 5.5
_exptl_crystal_grow.pdbx_details '0.4uL protein, 0.4 uL 100mM Bis-Tri pH 5.5, 25% PEG 3350, 0.2M NaCl equilibrated against a well of 0.5M LiCl'
_exptl_crystal_grow.temp 298
PDBx/mmCIF category Legacy PDB format records Description
_exptl_crystal REMARK 280 Results of experimental measurements on the crystal or crystals used, such as shape, size or density.

Example:

_exptl_crystal.density_Matthews 2.16
_exptl_crystal.density_percent_sol 43.08
_exptl_crystal.id 1

Data collection

PDBx/mmCIF category Legacy PDB format records Description
_diffrn REMARK 200 Details about the diffraction experiment ambient conditions.

Example:

_diffrn.id 1
_diffrn.ambient_temp 100
_diffrn.crystal_id 1
_diffrn.details ?
_diffrn.pdbx_serial_crystal_experiment N
PDBx/mmCIF category Legacy PDB format records Description
_diffrn_detector REMARK 200 Details about the detector used to measure the scattered radiation, including any analyser and post-sample collimation.

Example:

_diffrn_detector.diffrn_id 1
_diffrn_detector.details mirrors
_diffrn_detector.detector PIXEL
_diffrn_detector.type 'DECTRIS EIGER X 16M'
_diffrn_detector.pdbx_collection_date 2022-10-07
PDBx/mmCIF category Legacy PDB format records Description
_diffrn_radiation REMARK 200 Details about the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample.

Example:

_diffrn_radiation.diffrn_id 1
_diffrn_radiation.monochromomator 'Si (111)'
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
PDBx/mmCIF category Legacy PDB format records Description
_diffrn_radiation_wavelength REMARK 200 Details about the wavelength of the radiation used to measure the diffraction intensities. Several wavelengths can be provided here to describe for example multi-wavelength experiments, such as MAD.

Example:

loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
1 1.0 1.0
2 0.9793 1.0
PDBx/mmCIF category Legacy PDB format records Description
_diffrn_source REMARK 200 Details of the source of radiation used in the diffraction experiment.

Example:

_diffrn_source.current ?
_diffrn_source.details ?
_diffrn_source.diffrn_id 1
_diffrn_source.power ?
_diffrn_source.size ?
_diffrn_source.source SYNCHROTRON
_diffrn_source.target ?
_diffrn_source.type 'NSLS-II BEAMLINE 17-ID-2'
_diffrn_source.voltage ?
_diffrn_source.pdbx_wavelength_list 0.9793
_diffrn_source.pdbx_synchrotron_beamline 17-ID-2
_diffrn_source.pdbx_synchrotron_site NSLS-II
PDBx/mmCIF category Legacy PDB format records Description
_software
  • REMARK 3
  • REMARK 200
Details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation.

Example:

loop_
_software.citation_id
_software.classification
_software.compiler_name
_software.compiler_version
_software.contact_author
_software.contact_author_email
_software.date
_software.description
_software.dependencies
_software.hardware
_software.language
_software.location
_software.mods
_software.name
_software.os
_software.os_version
_software.type
_software.version
_software.pdbx_ordinal
? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1
? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALA ? ? ? . 2
? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3
? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4

Data collection and processing statistics

PDBx/mmCIF category Legacy PDB format records Description
_reflns REMARK 200 Overall data collection statistics for the X-ray diffraction experiment.

Example:

_reflns.d_resolution_high 1.660
_reflns.d_resolution_low 62.942
_reflns.pdbx_number_measured_all 560202
_reflns.number_obs 112977
_reflns.pdbx_Rmerge_I_obs 0.040
_reflns.pdbx_netI_over_sigmaI 17.990
_reflns.pdbx_chi_squared 1.115
_reflns.percent_possible_obs 99.400
_reflns.observed_criterion_sigma_I -3.000
_reflns.pdbx_Rrim_I_all 0.045
_reflns.pdbx_CC_half 0.999
_reflns.B_iso_Wilson_estimate 38.223
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.entry_id 7GT6
_reflns.observed_criterion_sigma_F ?
_reflns.number_all ?
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_redundancy ?
PDBx/mmCIF category Legacy PDB format records Description
_reflns_shell REMARK 200 Data collection statistics for the X-ray diffraction experiment broken into resolution shells.

Example:

loop_
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_ordinal
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.number_measured_obs
_reflns_shell.number_measured_all
_reflns_shell.number_unique_obs
_reflns_shell.pdbx_rejects
_reflns_shell.Rmerge_I_obs
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.pdbx_Rsym_value
_reflns_shell.pdbx_chi_squared
_reflns_shell.pdbx_redundancy
_reflns_shell.percent_possible_obs
_reflns_shell.pdbx_netI_over_sigmaI_obs
_reflns_shell.number_possible
_reflns_shell.number_unique_all
_reflns_shell.Rmerge_F_all
_reflns_shell.Rmerge_F_obs
_reflns_shell.Rmerge_I_all
_reflns_shell.meanI_over_sigI_all
_reflns_shell.percent_possible_all
_reflns_shell.pdbx_Rrim_I_all
_reflns_shell.pdbx_Rpim_I_all
_reflns_shell.pdbx_CC_half
1 1 1.660 1.760 73562 ? 18124 0 0.896 1.320 ? ? ? ? ? 18441 ? ? ? ? ? 98.300 1.035 ? 0.529
1 2 1.760 1.890 73368 ? 17113 0 0.473 2.780 ? ? ? ? ? 17267 ? ? ? ? ? 99.100 0.538 ? 0.845
1 3 1.890 2.040 83887 ? 15933 0 0.253 5.910 ? ? ? ? ? 16040 ? ? ? ? ? 99.300 0.282 ? 0.968
1 4 2.040 2.230 77815 ? 14753 0 0.130 11.180 ? ? ? ? ? 14824 ? ? ? ? ? 99.500 0.144 ? 0.990
1 5 2.230 2.490 69475 ? 13360 0 0.079 17.740 ? ? ? ? ? 13398 ? ? ? ? ? 99.700 0.088 ? 0.996
1 6 2.490 2.880 62385 ? 11722 0 0.050 27.680 ? ? ? ? ? 11738 ? ? ? ? ? 99.900 0.056 ? 0.998
1 7 2.880 3.520 52823 ? 9992 0 0.032 42.650 ? ? ? ? ? 9997 ? ? ? ? ? 99.900 0.036 ? 0.999
1 8 3.520 4.970 40142 ? 7731 0 0.024 57.810 ? ? ? ? ? 7734 ? ? ? ? ? 100.000 0.027 ? 0.999
1 9 4.920 62.942 22745 ? 4249 0 0.023 62.870 ? ? ? ? ? 4252 ? ? ? ? ? 99.900 0.025 ? 0.999

Refinement

PDBx/mmCIF category Legacy PDB format records Description
_refine REMARK 3 Details about the structure-refinement statistics.

Example:

_refine.entry_id 7GT6
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.ls_d_res_high 1.6600
_refine.ls_d_res_low 62.9400
_refine.pdbx_ls_sigma_F 0.000
_refine.ls_percent_reflns_obs 99.3700
_refine.ls_number_reflns_obs 56491
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.pdbx_R_Free_selection_details RANDOM
_refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY'
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs 0.2007
_refine.ls_R_factor_R_word 0.1996
_refine.ls_R_factor_R_free 0.2276
_refine.ls_percent_reflns_R_free 3.9000
_refine.ls_number_reflns_R_free 2321
_refine.B_iso_mean 37.3880
_refine.aniso_B[1][1] 0.5500
_refine.aniso_B[2][2] 0.5500
_refine.aniso_B[3][3] -1.7900
_refine.aniso_B[1][2] 0.2800
_refine.aniso_B[1][3] 0.0000
_refine.aniso_B[2][3] 0.0000
_refine.correlation_coeff_Fo_to_Fc 0.9620
_refine.correlation_coeff_Fo_to_Fc_free 0.9530
_refine.pdbx_overall_ESU_R 0.0890
_refine.pdbx_overall_ESU_R_Free 0.0900
_refine.overall_SU_ML 0.0740
_refine.overall_SU_B 2.3210
_refine.solvent_model_details MASK
_refine.pdbx_solvent_vdw_probe_radii 1.2000
_refine.pdbx_solvent_ion_probe_radii 0.8000
_refine.pdbx_solvent_shrinkage_radii 0.8000
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.B_iso_max 135.070
_refine.B_iso_min 19.500
_refine.pdbx_diffrn_id 1
PDBx/mmCIF category Legacy PDB format records Description
_refine_ls_shell REMARK 3 Details about the results of the least-squares refinement broken down into shells of resolution.

Example:

loop_
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.pdbx_total_number_of_bins_used
_refine_ls_shell.percent_reflns_obs
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_all
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.R_factor_R_free
_refine_ls_shell.percent_reflns_R_free
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.R_factor_R_free_error
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.redundancy_reflns_obs
_refine_ls_shell.pdbx_refine_id
2.500 2.6316 7 97.0 4166 . 0.4102 0.4078 . 135 . 4301 4301 . 'X-RAY DIFFRACTION'
2.6316 2.7964 7 100.0 4242 . 0.3417 0.3548 . 156 . 4398 4398 . 'X-RAY DIFFRACTION'
2.7964 3.0123 7 100.0 4332 . 0.2683 0.3923 . 113 . 4445 4445 . 'X-RAY DIFFRACTION'
3.0123 3.3153 7 100.0 4285 . 0.2135 0.2780 . 158 . 4443 4443 . 'X-RAY DIFFRACTION'
3.3153 3.7947 7 98.0 4266 . 0.2193 0.2524 . 137 . 4403 4403 . 'X-RAY DIFFRACTION'
3.7947 4.7796 7 99.0 4312 . 0.1696 0.2265 . 156 . 4468 4468 . 'X-RAY DIFFRACTION'
4.7796 39.7236 7 100.0 4512 . 0.1794 0.1675 . 160 . 4672 4672 . 'X-RAY DIFFRACTION'
PDBx/mmCIF category Legacy PDB format records Description
_refine_ls_restr REMARK 3 Details about the restraints applied to various classes of parameters during the least-squares refinement.

Notes:

Example:

loop_
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.pdbx_restraint_function
'X-RAY DIFFRACTION' r_bond_refined_d 3714 0.048 0.025 ? ?
'X-RAY DIFFRACTION' r_bond_other_d 2730 0.001 0.015 ? ?
'X-RAY DIFFRACTION' r_angle_refined_deg 3919 1.717 1.662 ? ?
'X-RAY DIFFRACTION' r_angle_other_deg 6334 1.410 1.601 ? ?
'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 355 6.689 5.000 ? ?
'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 169 29.721 21.361 ? ?
'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 545 14.366 15.000 ? ?
'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 26 24.117 15.000 ? ?
'X-RAY DIFFRACTION' r_chiral_restr 357 0.088 0.200 ? ?
'X-RAY DIFFRACTION' r_gen_planes_refined 3323 0.009 0.020 ? ?
'X-RAY DIFFRACTION' r_gen_planes_other 705 0.001 0.020 ? ?
'X-RAY DIFFRACTION' r_mcbond_it 1792 3.161 3.442 ? ?
'X-RAY DIFFRACTION' r_mcbond_other 1753 3.149 3.416 ? ?
'X-RAY DIFFRACTION' r_mcangle_it 1735 4.416 5.214 ? ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_initial_refinement_model N/A The starting model(s) used in structure determination.

Example:

_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.entity_id_list 1
_pdbx_initial_refinement_model.type 'experimental model'
_pdbx_initial_refinement_model.source_name PDB
_pdbx_initial_refinement_model.accession_code 6HA3
_pdbx_initial_refinement_model.details ?

Crystallographic and Coordinate Transformation Section

PDBx/mmCIF category Legacy PDB format records Description
_symmetry CRYST1 Details about the space group symmetry.

Example:

_symmetry.entry_id 8VCW
_symmeetry.cell_setting ?
_symmetry.Int_Tables_number 19
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmeetry.pdbx_full_space_group_name_H-M ?
PDBx/mmCIF category Legacy PDB format records Description
_cell CRYST1 Details about the crystallographic cell parameters.

Example:

_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.entry_id 8VCW
_cell.length_a 38.209
_cell.length_b 50.7776
_cell.length_c 161.878
_cell.Z_PDB 4
PDBx/mmCIF category Legacy PDB format records Description
_atom_sites SCALE Details about the matrix used to transform fractional coordinates to Cartesian coordinates.

Example:

_atom_sites.entry_id 8VCW
_atom_sites.Cartn_transf_matrix[1][1] ?
_atom_sites.Cartn_transf_matrix[1][2] ?
_atom_sites.Cartn_transf_matrix[1][3] ?
_atom_sites.Cartn_transf_matrix[2][1] ?
_atom_sites.Cartn_transf_matrix[2][2] ?
_atom_sites.Cartn_transf_matrix[2][3] ?
_atom_sites.Cartn_transf_matrix[3][1] ?
_atom_sites.Cartn_transf_matrix[3][2] ?
_atom_sites.Cartn_transf_matrix[3][3] ?
_atom_sites.Cartn_transf_vector[1] ?
_atom_sites.Cartn_transf_vector[2] ?
_atom_sites.Cartn_transf_vector[3] ?
_atom_sites.Cart_transform_axes ?
_atom_sites.fract_transf_matrix[1][1] 0.026172
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.019694
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.006177
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000

Information Specific To Electron Microscopy (3DEM)

Sample Description

PDBx/mmCIF category Legacy PDB format records Description
_em_entity_assembly REMARK 245 Details about each component of the complex.

Notes:

  • An isolated protein would be classified in _em_entity_assembly.type as "COMPLEX". The other categories refer to large-scale samples, such as "CELL", "VIRUS", etc.

Example:

_em_entity_assembly.id 1
_em_entity_assembly.parent_id 0
_em_entity_assembly.source RECOMBINANT
_em_entity_assembly.type COMPLEX
_em_entity_assembly.name 'Core tetramer assembly (p2) of the phiPA3 bacteriophage PhuN protein'
_em_entity_assembly.details ?
_em_entity_assembly.synonym ?
_em_entity_assembly.oligomeric_details ?
_em_entity_assembly.entity_id_list 1
PDBx/mmCIF category Legacy PDB format records Description
_em_entity_assembly_molwt N/A Details about the molecular weight of an assembly component of the sample.

Example:

loop_
_em_entity_assembly_molwt.entity_assembly_id
_em_entity_assembly_molwt.id
_em_entity_assembly_molwt.units
_em_entity_assembly_molwt.value
1 1 MEGADALTONS 30.5
PDBx/mmCIF category Legacy PDB format records Description
_em_entity_assembly_naturalsource N/A Details about the natural source for EM assemblies and assembly components.

Example:

_em_entity_assembly_naturalsource.cell ?
_em_entity_assembly_naturalsource.cellular_location ?
_em_entity_assembly_naturalsource.entity_assembly_id 1
_em_entity_assembly_naturalsource.id 2
_em_entity_assembly_naturalsource.ncbi_tax_id 998086
_em_entity_assembly_naturalsource.organism 'Pseudomonas phage PhiPA3'
_em_entity_assembly_naturalsource.organelle ?
_em_entity_assembly_naturalsource.organ ?
_em_entity_assembly_naturalsource.strain ?
_em_entity_assembly_naturalsource.tissue ?
PDBx/mmCIF category Legacy PDB format records Description
_em_entity_assembly_recombinant N/A Details about the recombinant expression of the assembly or assembly component.

Example:

_em_entity_assembly_recombinant.cell ?
_em_entity_assembly_recombinant.entity_assembly_id 1
_em_entity_assembly_recombinant.id 2
_em_entity_assembly_recombinant.ncbi_tax_id 562
_em_entity_assembly_recombinant.organism 'Escherichia coli'
_em_entity_assembly_recombinant.plasmid ?
_em_entity_assembly_recombinant.strain 'BL21 Star (DE3)pLysS'

EM Experiment

PDBx/mmCIF category Legacy PDB format records Description
_em_experiment REMARK 245 High-level classification of the EM experiment.

Example:

_em_experiment.entry_id 8FNE
_em_experiment.id 1
_em_experiment.reconstruction_method 'SINGLE PARTICLE'
_em_experiment.aggregation_state '2D ARRAY'
_em_experiment.entity_assembly_id 1

Sample preparation

PDBx/mmCIF category Legacy PDB format records Description
_em_specimen REMARK 245 Details about specimens prepared for imaging by electron microscopy.

Example:

_em_specimen.concentration ?
_em_specimen.details ?
_em_specimen.embedding_applied NO
_em_specimen.experiment_id 1
_em_specimen.id 1
_em_specimen.shadowing_applied NO
_em_specimen.staining_applied NO
_em_specimen.vitrification_applied YES
PDBx/mmCIF category Legacy PDB format records Description
_em_buffer REMARK 245 Details of the sample buffer.

Example:

_em_buffer.id 1
_em_buffer.specimen_id 1
_em_buffer.name ?
_em_buffer.details '0.25 complete Protease Inhibitor Tablet also included'
_em_buffer.pH 6.5
PDBx/mmCIF category Legacy PDB format records Description
_em_buffer_component N/A Details of the sample buffer components.

Example:

loop_
_em_buffer_component.buffer_id
_em_buffer_component.concentration
_em_buffer_component.concentration_units
_em_buffer_component.formula
_em_buffer_component.id
_em_buffer_component.name
1 20 mM ? 1 BisTrisPropane
1 150 mM ? 2 'Sodium Chloride'
1 1 mM ? 3 DTT
1 1 mM ? 4 EDTA
1 2 mM ? 5 'Magnesium Chloride'
1 1 mM ? 6 ATP
PDBx/mmCIF category Legacy PDB format records Description
_em_staining N/A Details about the staining procedure used in the specimen preparation.

Example:

_em_staining.id 1
_em_staining.specimen_id 1
_em_staining.material 'Uranyl Acetate'
_em_staining.type NEGATIVE
_em_staining.details 'Negatively stained EM specimens were prepared using a carbon-sandwich technique and uranyl-acetate stain.'
PDBx/mmCIF category Legacy PDB format records Description
_em_embedding N/A Details about the embedding procedure used in the specimen preparation.

Example:

_em_embedding.details '3% trehalose'
_em_embedding.id 1
_em_embedding.material trehalose
_em_embedding.specimen_id 1
PDBx/mmCIF category Legacy PDB format records Description
_em_shadowing N/A Details about the shadowing of an EM specimen.

Example:

_em_shadowing.id 1
_em_shadowing.specimen_id 1
_em_shadowing.angle 45
_em_shadowing.thickness 3
_em_shadowing.material Platinum
_em_shadowing.details 'shadowing was used to create a platinum replica'
PDBx/mmCIF category Legacy PDB format records Description
_em_sample_support REMARK 245 Details of the electron microscope grid type, grid support film and pretreatment of the whole before sample is applied.

Example:

_em_sample_support.id 1
_em_sample_support.film_material 'HOLEY CARBON'
_em_sample_support.grid_material COPPER
_em_sample_support.grid_mesh_size 400
_em_sample_support.details 'GLOW DISCHARGED 120 seconds'
PDBx/mmCIF category Legacy PDB format records Description
_em_support_film N/A Describes films supporting the specimen.

Example:

_em_support_film.id 1
_em_support_film.material CARBON
PDBx/mmCIF category Legacy PDB format records Description
_em_grid_pretreatment N/A Describes glow discharge pretreatment for an EM grid.

Example:

_em_grid_pretreatment.id 1
_em_grid_pretreatment.sample_support_id 1
_em_grid_pretreatment.type 'GLOW DISCHARGE'
_em_grid_pretreatment.time 12
PDBx/mmCIF category Legacy PDB format records Description
_em_vitrification REMARK 245 Details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope.

Example:

_em_vitrification.entry_id 8FNE
_em_vitrification.id 1
_em_vitrification.specimen_id 1
_em_vitrification.cryogen_name ETHANE
_em_vitrification.humidity 100
_em_vitrification.temp ?
_em_vitrification.chamber_temperature 283.15
_em_vitrification.instrument 'FEI VITROBOT MARK IV'
_em_vitrification.method ?
_em_vitrification.time_resolved_state ?
_em_vitrification.citation_id ?
_em_vitrification.details ?

Imaging

PDBx/mmCIF category Legacy PDB format records Description
_em_imaging REMARK 245 Details about the parameters used in imaging the sample in the electron microscope.

Example:

_em_imaging.entry_id 8FNE
_em_imaging.id 1
_em_imaging.microscope_model 'FEI TITAN KRIOS'
_em_imaging.specimen_holder_type ?
_em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER'
_em_imaging.accelerating_voltage 300
_em_imaging.illumination_mode 'FLOOD BEAM'
_em_imaging.mode 'BRIGHT FIELD'
_em_imaging.nominal_cs 2.7
_em_imaging.nominal_defocus_min 800
_em_imaging.nominal_defocus_max 2500
_em_imaging.nominal_magnification 105000
_em_imaging.electron_source 'FIELD EMISSION GUN'
_em_imaging.specimen_id 1
_em_imaging.cryogen NITROGEN
PDBx/mmCIF category Legacy PDB format records Description
_em_image_scans REMARK 245 Details of the image scanning device (microdensitometer) and parameters for digitization of the image.

Example:

_em_image_scans.entry_id 1DYL
_em_image_scans.id 2
_em_image_scans.number_digital_images 48
PDBx/mmCIF category Legacy PDB format records Description
_em_tomography N/A Microscopy parameters only relevant for tomography.

Example:

_em_tomography.id 1
_em_tomography.imaging_id 1
_em_tomography.dual_tilt_axis_rotation 90.0
_em_tomography.axis1_angle_increment 2
_em_tomography.axis1_min_angle -70.00
_em_tomography.axis1_max_angle 70.0
_em_tomography.axis2_angle_increment 2
_em_tomography.axis2_min_angle -70.0
_em_tomography.axis2_max_angle 70.0
PDBx/mmCIF category Legacy PDB format records Description
_em_imaging_optics N/A Description of a few specialist optics apparatus.

Example:

_em_imaging_optics.id 1
_em_imaging_optics.imaging_id 1
_em_imaging_optics.chr_aberration_corrector 'CEOS manufactured Cc corrector'
_em_imaging_optics.energyfilter_lower 0
_em_imaging_optics.energyfilter_upper 15
_em_imaging_optics.energyfilter_name FEI
_em_imaging_optics.phase_plate ?
_em_imaging_optics.sph_aberration_corrector ?
PDBx/mmCIF category Legacy PDB format records Description
_em_focused_ion_beam N/A Description of sectioning by focused_ion_beam.

Example:

No example available
PDBx/mmCIF category Legacy PDB format records Description
_em_image_recording REMARK 245 Details of the image recording (either film/microdensitometer or electronic densitometer) and parameters for image digitization.

Example:

_em_image_recording.average_exposure_time ?
_em_image_recording.avg_electron_dose_per_subtomogram ?
_em_image_recording.avg_electron_dose_per_image 67
_em_image_recording.details ?
_em_image_recording.detector_mode ?
_em_image_recording.film_or_detector_model 'GATAN K3 BIOQUANTUM (6k x 4k)'
_em_image_recording.id 1
_em_image_recording.imaging_id 1
_em_image_recording.num_diffraction_images ?
_em_image_recording.num_grids_imaged ?
_em_image_recording.num_real_images ?

Reconstruction

PDBx/mmCIF category Legacy PDB format records Description
_em_3d_reconstruction
  • REMARK 3
  • REMARK 245
Details of the 3D reconstruction procedure from 2D projections.

Example:

_em_3d_reconstruction.entry_id 8FNE
_em_3d_reconstruction.id 1
_em_3d_reconstruction.method ?
_em_3d_reconstruction.algorithm ?
_em_3d_reconstruction.citation_id ?
_em_3d_reconstruction.details ?
_em_3d_reconstruction.resolution 3.9
_em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF'
_em_3d_reconstruction.magnification_calibration ?
_em_3d_reconstruction.nominal_pixel_size ?
_em_3d_reconstruction.actual_pixel_size ?
_em_3d_reconstruction.num_particles 29303
_em_3d_reconstruction.euler_angles_details ?
_em_3d_reconstruction.num_class_averages ?
_em_3d_reconstruction.refinement_type ?
_em_3d_reconstruction.image_processing_id 1
_em_3d_reconstruction.symmetry_type POINT
PDBx/mmCIF category Legacy PDB format records Description
_em_particle_selection N/A Details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.

Example:

_em_particle_selection.id 1
_em_particle_selection.image_processing_id 1
_em_particle_selection.num_particles_selected 5267
_em_particle_selection.method 'INTERACTIVE'
_em_particle_selection.details ?
PDBx/mmCIF category Legacy PDB format records Description
_em_image_processing N/A Details of the EM image processing procedure.

Example:

_em_image_processing.id 1
_em_image_processing.image_recording_id 1
_em_image_processing.details 'The selected images were high-pass filtered and normalized'
PDBx/mmCIF category Legacy PDB format records Description
_em_ctf_correction N/A Description of the Contrast Transfer Function (CTF) correction.

Example:

_em_ctf_correction.details ?
_em_ctf_correction.id 1
_em_ctf_correction.em_image_processing_id 1
_em_ctf_correction.type 'PHASE FLIPPING ONLY'

Symmetry

PDBx/mmCIF category Legacy PDB format records Description
_em_helical_entity N/A Details for a helical or filament type of assembly component.

Example:

_em_helical_entity.id 1
_em_helical_entity.image_processing_id 1
_em_helical_entity.details ?
_em_helical_entity.axial_symmetry C2
_em_helical_entity.angular_rotation_per_subunit -0.782
_em_helical_entity.axial_rise_per_subunit 4.763
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_helical_symmetry N/A Details about the helical symmetry group associated with this entry.

Example:

_pdbx_helical_symmetry.entry_id '1ABC'
_pdbx_helical_symmetry.number_of_operations 35
_pdbx_helical_symmetry.rotation_per_n_subunits 131.84
_pdbx_helical_symmetry.rise_per_n_subunits 6.10
_pdbx_helical_symmetry.n_subunits_divisor 1
_pdbx_helical_symmetry.dyad_axis no
_pdbx_helical_symmetry.circular_symmetry 1
PDBx/mmCIF category Legacy PDB format records Description
_em_single_particle_entity N/A Details of the enforced symmetry for a single particle entity type.

Example:

_em_single_particle_entity.entry_id 8GA0
_em_single_particle_entity.id 1
_em_single_particle_entity.image_processing_id 1
_em_single_particle_entity.point_symmetry C1

Fitting

PDBx/mmCIF category Legacy PDB format records Description
_em_3d_fitting REMARK 3 Details of the method of fitting atomic coordinates from a coordinate file into a 3d-em volume map file.

Example:

_em_3d_fitting.id 1
_em_3d_fitting.entry_id 8FNE
_em_3d_fitting.method ?
_em_3d_fitting.target_criteria ?
_em_3d_fitting.details 'The initial model was generated using AlphaFold based on sequence alone.'
_em_3d_fitting.overall_b_value ?
_em_3d_fitting.ref_space ?
_em_3d_fitting.ref_protocol 'FLEXIBLE FIT'
PDBx/mmCIF category Legacy PDB format records Description
_em_3d_fitting_list N/A Details of the initial model used in fitting.

Example:

_em_3d_fitting_list.id 1
_em_3d_fitting_list.3d_fitting_id 1
_em_3d_fitting_list.pdb_entry_id ?
_em_3d_fitting_list.pdb_chain_id ?
_em_3d_fitting_list.pdb_chain_residue_range ?
_em_3d_fitting_list.details ?
_em_3d_fitting_list.chain_id ?
_em_3d_fitting_list.chain_residue_range ?
_em_3d_fitting_list.source_name AlphaFold
_em_3d_fitting_list.type 'in silico model'
_em_3d_fitting_list.accession_code ?

Software

PDBx/mmCIF category Legacy PDB format records Description
_em_software REMARK 3 Details of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.

Example:

loop_
_em_software.category
_em_software.details
_em_software.id
_em_software.image_processing_id
_em_software.fitting_id
_em_software.imaging_id
_em_software.name
_em_software.version
'PARTICLE SELECTION' ? 1 1 ? ? cryoSPARC v2.15.0
'PARTICLE SELECTION' ? 2 1 ? ? cryoSPARC v3.3.1
'PARTICLE SELECTION' ? 3 1 ? ? ? ?
'IMAGE ACQUISITION' ? 4 ? ? 1 SerialEM v.3.6-v.3.8
MASKING ? 5 ? ? ? ? ?
'CTF CORRECTION' ? 6 1 ? ? ? ?
'LAYERLINE INDEXING' ? 7 1 ? ? ? ?
'DIFFRACTION INDEXING' ? 8 1 ? ? ? ?
'MODEL FITTING' RosettaRelax 9 ? 1 ? Rosetta ?
'MODEL FITTING' ? 10 ? 1 ? 'UCSF ChimeraX' ?
'MODEL FITTING' ? 11 ? 1 ? 'UCSF Chimera' ?
OTHER ? 12 ? ? ? ? ?
'IMAGE ACQUISITION' ? 13 ? ? ? ? ?
'MODEL REFINEMENT' RosettaRefine 14 ? 1 ? Rosetta ?
'MODEL REFINEMENT' ? 15 ? 1 ? ISOLDE 1.2.1
'INITIAL EULER ASSIGNMENT' 'Ab-Initio Reconstruction' 16 1 ? ? cryoSPARC v2.15.0
'INITIAL EULER ASSIGNMENT' ? 17 1 ? ? ? ?
'FINAL EULER ASSIGNMENT' ? 18 1 ? ? cisTEM 1.0.0-beta
'FINAL EULER ASSIGNMENT' ? 19 1 ? ? ? ?
CLASSIFICATION ? 20 1 ? ? cisTEM 1.0.0-beta
CLASSIFICATION ? 21 1 ? ? ? ?
RECONSTRUCTION ? 22 1 ? ? ? ?

Information Specific To Nuclear Magnetic Resonance (NMR)

Ensemble Description

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_ensemble REMARK 210 Describes the ensemble of deposited structures.

Example:

_pdbx_nmr_ensemble.entry_id 8COO
_pdbx_nmr_ensemble.conformers_calculated_total_number 40
_pdbx_nmr_ensemble.conformers_submitted_total_number 20
_pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy'
_pdbx_nmr_ensemble.representative_conformer ?
_pdbx_nmr_ensemble.average_constraints_per_residue ?
_pdbx_nmr_ensemble.average_constraint_violations_per_residue ?
_pdbx_nmr_ensemble.maximum_distance_constraint_violation ?
_pdbx_nmr_ensemble.average_distance_constraint_violation ?
_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ?
_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ?
_pdbx_nmr_ensemble.distance_constraint_violation_method ?
_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ?
_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ?
_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_representative REMARK 210 Describes selection of the representative structure.

Example:

_pdbx_nmr_representative.entry_id 8COO
_pdbx_nmr_representative.conformer_id 1
_pdbx_nmr_representative.selection_criteria 'lowest energy'

Sample Preparation

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_sample_details REMARK 210 Complete description of each NMR sample, including the solvent system used.

Example:

_pdbx_nmr_sample_details.solution_id 1
_pdbx_nme_sample_details.contents '300 uM [U-100% 13C; U-100% 15N] sample 1, 95% H2O/5% D2O'
_pdbx_nmr_sample_details.solvent_system '95% H2O/5% D2O'
_pdbx_nmr_sample_details.label 13C15N_sample
_pdbx_nmr_sample_details.type solution
_pdbx_nmr_sample_details.details ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_exptl_sample N/A The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name.

Example:

_pdbx_nmr_exptl_sample.solution_id 1
_pdbx_nmr_exptl_sample.component 'sample 1'
_pdbx_nmr_exptl_sample.concentration 300
_pdbx_nmr_exptl_sample.concentration_range ?
_pdbx_nmr_exptl_sample.concentration_units uM
_pdbx_nmr_exptl_sample.isotopic_labeling '[U-100% 13C; U-100% 15N]'
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_exptl_sample_conditions REMARK 210 The experimental conditions used for each sample. Each set of conditions is identified by a numerical code.

Example:

_pdbx_nmr_exptl_sample_conditions.conditions_id 1
_pdbx_nmr_exptl_sample_conditions.temperature 310
_pdbx_nmr_exptl_sample_conditions.pressure_units atm
_pdbx_nmr_exptl_sample_conditions.pressure ambient
_pdbx_nmr_exptl_sample_conditions.pH 6.5
_pdbx_nmr_exptl_sample_conditions.ionic_strength 0.02
_pdbx_nmr_exptl_sample_conditions.details '0.3 mM [U-100% 13C; U-100% 15N]'
_pdbx_nmr_exptl_sample_conditions.ionic_strength_err ?
_pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined'
_pdbx_nmr_exptl_sample_conditions.label 13C15N_sample
_pdbx_nmr_exptl_sample_conditions.pH_err ?
_pdbx_nmr_exptl_sample_conditions.pH_units pH
_pdbx_nmr_exptl_sample_conditions.pressure_err ?
_pdbx_nmr_exptl_sample_conditions.temperature_err ?
_pdbx_nmr_exptl_sample_conditions.temperature_units K

Data Collection

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_spectrometer REMARK 210 Details about each spectrometer used to collect data for this deposition.

Example:

loop_
_pdbx_nmr_spectrometer.spectrometer_id
_pdbx_nmr_spectrometer.model
_pdbx_nmr_spectrometer.type
_pdbx_nmr_spectrometer.manufacturer
_pdbx_nmr_spectrometer.field_strength
_pdbx_nmr_spectrometer.details
1 'AVANCE III' ? Bruker 600 ?
2 'AVANCE III' ? Bruker 850 ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_exptl REMARK 210 Information on the experiments that were used to generate constraint data.

Example:

loop_
_pdbx_nmr_exptl.experiment_id
_pdbx_nmr_exptl.conditions_id
_pdbx_nmr_exptl.solution_id
_pdbx_nmr_exptl.type
_pdbx_nmr_exptl.spectrometer_id
_pdbx_nmr_exptl.sample_state
1 1 1 '2D 1H-15N HSQC' 1 isotropic
2 1 1 '2D 1H-13C HSQC' 1 isotropic
3 1 1 '3D 1H-13C NOESY aliphatic' 1 isotropic
4 1 1 '3D 1H-15N NOESY' 1 isotropic
5 1 1 '2D 1H-1H NOESY' 2 isotropic
6 1 1 '2D 1H-1H NOESY' 3 isotropic

Refinement

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_refine REMARK 210 Method and details of the refinement of the deposited structure.

Example:

_pdbx_nmr_refine.entry_id 8COO
_pdbx_nmr_refine.method 'torsion angle dynamics'
_pdbx_nmr_refine.details ?
_pdbx_nmr_refine.software_ordinal 1

Software

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_nmr_software
  • REMARK 3
  • REMARK 210
Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.

Example:

loop_
_pdbx_nmr_software.ordinal
_pdbx_nmr_software.classification
_pdbx_nmr_software.name
_pdbx_nmr_software.version
_pdbx_nmr_software.authors
1 refinement ARIA ?
;Linge, O'Donoghue and Nilges
;
2 'structure calculation' ARIA ?
;Linge, O'Donoghue and Nilges
;
3 'chemical shift assignment' XEASY ? 'Bartels et al.'
4 'peak picking' XEASY ? 'Bartels et al.'

ASSEMBLY

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_struct_assembly REMARK 350 Details about the structural elements that form macromolecular assemblies.

Example:

_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details dimeric
_pdbx_struct_assembly.oligomeric_count 2
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_struct_assembly_gen REMARK 350 Details about the generation of each macromolecular assembly.

Notes:

Example:

_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1,2
_pdbx_struct_assembly_gen.asym_id_list A,B,C,D
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_struct_assembly_prop REMARK 350 Details about the calculated total surface area, buried surface area and free energy gain for an assembly.

Example:

loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
1 'ABSA (A^2)' 3090 ?
1 MORE -33 ?
1 'SSA (A^2)' 25780 ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_struct_oper_list REMARK 350 Details about the symmetry operations and Cartesian rotation and translation matrices required to transform the coordinates deposited with the entry to generate the biological assembly.

Example:

loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
2 'crystal symmetry operation' 2_555 -x,-y,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000

SECONDARY STRUCTURE

PDBx/mmCIF category Legacy PDB format records Description
_struct_conf_type HELIX Type of the conformation of the backbone of the polymer.

Example:

_struct_conf_type.id HELX_P
PDBx/mmCIF category Legacy PDB format records Description
_struct_conf HELIX Details about the backbone conformation of a segment of polymer.

Example:

loop_
_struct_conf.conf_type_id
_struct_conf.id
_struct_conf.pdbx_PDB_helix_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.pdbx_beg_PDB_ins_code
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.pdbx_end_PDB_ins_code
_struct_conf.beg_auth_comp_id
_struct_conf.beg_auth_asym_id
_struct_conf.beg_auth_seq_id
_struct_conf.end_auth_comp_id
_struct_conf.end_auth_asym_id
_struct_conf.end_auth_seq_id
_struct_conf.pdbx_PDB_helix_class
_struct_conf.details
_struct_conf.pdbx_PDB_helix_length
HELX_P HELX_P1 AA1 SER A 10 ? GLY A 15 ? SER A 10 GLY A 15 1 ? 6
HELX_P HELX_P2 AA2 HIS A 41 ? CYS A 44 ? HIS A 41 CYS A 44 5 ? 4
HELX_P HELX_P3 AA3 GLU A 47 ? ASN A 51 ? GLU A 47 ASN A 51 5 ? 5
HELX_P HELX_P4 AA4 ASN A 53 ? ARG A 60 ? ASN A 53 ARG A 60 1 ? 8
HELX_P HELX_P5 AA5 LYS A 61 ? HIS A 64 ? LYS A 61 HIS A 64 5 ? 4
HELX_P HELX_P6 AA6 ILE A 200 ? ASN A 214 ? ILE A 200 ASN A 214 1 ? 15
HELX_P HELX_P7 AA7 THR A 226 ? TYR A 237 ? THR A 226 TYR A 237 1 ? 12
HELX_P HELX_P8 AA8 THR A 243 ? LEU A 250 ? THR A 243 LEU A 250 1 ? 8
HELX_P HELX_P9 AA9 LEU A 250 ? GLY A 258 ? LEU A 250 GLY A 258 1 ? 9
HELX_P HELX_P10 AB1 ALA A 260 ? GLY A 275 ? ALA A 260 GLY A 275 1 ? 16
HELX_P HELX_P11 AB2 THR A 292 ? SER A 301 ? THR A 292 SER A 301 1 ? 10
PDBx/mmCIF category Legacy PDB format records Description
_struct_sheet SHEET Details about the beta sheets.

Example:

loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
AA1 ? 7 ?
AA2 ? 5 ?
AA3 ? 3 ?
PDBx/mmCIF category Legacy PDB format records Description
_struct_sheet_order SHEET Details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet.

Example:

loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
AA1 1 2 ? anti-parallel
AA1 2 3 ? anti-parallel
AA1 3 4 ? anti-parallel
AA1 4 5 ? anti-parallel
AA1 5 6 ? anti-parallel
AA1 6 7 ? anti-parallel
AA2 1 2 ? parallel
AA2 2 3 ? anti-parallel
AA2 3 4 ? anti-parallel
AA2 4 5 ? anti-parallel
AA3 1 2 ? parallel
AA3 2 3 ? anti-parallel
PDBx/mmCIF category Legacy PDB format records Description
_struct_sheet_range SHEET Details about the residue ranges that form a beta-sheet. Residues are included in a range if they make beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range.

Example:

loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.pdbx_beg_PDB_ins_code
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.pdbx_end_PDB_ins_code
_struct_sheet_range.beg_auth_comp_id
_struct_sheet_range.beg_auth_asym_id
_struct_sheet_range.beg_auth_seq_id
_struct_sheet_range.end_auth_comp_id
_struct_sheet_range.end_auth_asym_id
_struct_sheet_range.end_auth_seq_id
AA1 1 VAL A 73 ? LEU A 75 ? VAL A 73 LEU A 75
AA1 2 PHE A 66 ? ALA A 70 ? PHE A 66 ALA A 70
AA1 3 MET A 17 ? CYS A 22 ? MET A 17 CYS A 22
AA1 4 THR A 25 ? LEU A 32 ? THR A 25 LEU A 32
AA1 5 VAL A 35 ? PRO A 39 ? VAL A 35 PRO A 39
AA1 6 VAL A 86 ? VAL A 91 ? VAL A 86 VAL A 91
AA1 7 VAL A 77 ? GLN A 83 ? VAL A 77 GLN A 83
AA2 1 LYS A 100 ? PHE A 103 ? LYS A 100 PHE A 103
AA2 2 CYS A 156 ? GLU A 166 ? CYS A 156 GLU A 166
AA2 3 VAL A 148 ? ASP A 153 ? VAL A 148 ASP A 153
AA2 4 THR A 111 ? TYR A 118 ? THR A 111 TYR A 118
AA2 5 SER A 121 ? ALA A 129 ? SER A 121 ALA A 129
AA3 1 LYS A 100 ? PHE A 103 ? LYS A 100 PHE A 103
AA3 2 CYS A 156 ? GLU A 166 ? CYS A 156 GLU A 166
AA3 3 HIS A 172 ? THR A 175 ? HIS A 172 THR A 175
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_struct_sheet_hbond SHEET Details about the hydrogen bonding between residue ranges in a beta sheet.

Example:

loop_
_pdbx_struct_sheet_hbond.sheet_id
_pdbx_struct_sheet_hbond.range_id_1
_pdbx_struct_sheet_hbond.range_id_2
_pdbx_struct_sheet_hbond.range_1_label_atom_id
_pdbx_struct_sheet_hbond.range_1_label_comp_id
_pdbx_struct_sheet_hbond.range_1_label_asym_id
_pdbx_struct_sheet_hbond.range_1_label_seq_id
_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_pdbx_struct_sheet_hbond.range_1_auth_atom_id
_pdbx_struct_sheet_hbond.range_1_auth_comp_id
_pdbx_struct_sheet_hbond.range_1_auth_asym_id
_pdbx_struct_sheet_hbond.range_1_auth_seq_id
_pdbx_struct_sheet_hbond.range_2_label_atom_id
_pdbx_struct_sheet_hbond.range_2_label_comp_id
_pdbx_struct_sheet_hbond.range_2_label_asym_id
_pdbx_struct_sheet_hbond.range_2_label_seq_id
_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_pdbx_struct_sheet_hbond.range_2_auth_atom_id
_pdbx_struct_sheet_hbond.range_2_auth_comp_id
_pdbx_struct_sheet_hbond.range_2_auth_asym_id
_pdbx_struct_sheet_hbond.range_2_auth_seq_id
AA1 1 2 O LEU A 75 ? O LEU A 75 N VAL A 68 ? N VAL A 68
AA1 2 3 O LEU A 67 ? O LEU A 67 N THR A 21 ? N THR A 21
AA1 3 4 N VAL A 20 ? N VAL A 20 O LEU A 27 ? O LEU A 27
AA1 4 5 N LEU A 30 ? N LEU A 30 O TYR A 37 ? O TYR A 37
AA1 5 6 N CYS A 38 ? N CYS A 38 O LEU A 87 ? O LEU A 87
AA1 6 7 O LYS A 90 ? O LYS A 90 N ILE A 78 ? N ILE A 78
AA2 1 2 N LYS A 100 ? N LYS A 100 O VAL A 157 ? O VAL A 157
AA2 2 3 O SER A 158 ? O SER A 158 N ASN A 151 ? N ASN A 151
AA2 3 4 O PHE A 150 ? O PHE A 150 N SER A 113 ? N SER A 113
AA2 4 5 N ALA A 116 ? N ALA A 116 O SER A 123 ? O SER A 123
AA3 1 2 N LYS A 100 ? N LYS A 100 O VAL A 157 ? O VAL A 157
AA3 2 3 N MET A 165 ? N MET A 165 O ALA A 173 ? O ALA A 173

COORDINATE SECTION

PDBx/mmCIF category Legacy PDB format records Description
_atom_site
  • ATOM
  • HETATM
Details about the atoms in a macromolecular crystal structure, such as the positional coordinates, temperature factors, and occupancies.

Notes:

  • _atom_site.label_asym_id - ASYM ID, a unique and sequential identifier of each molecule (starting from letter A) in the model. This data item is a pointer to _struct_asym.id in the _struct_asym category.
    • ASYM_ID can be different from the author provided (or PDB assigned) chain identifier (Chain ID), ASYM_ID is assigned sequentially starting from letter A to all polymer and non-polymer molecule instances in the structure.
    • All water molecules are assigned one ASYM_ID.
  • _atom_site.auth_asym_id - author provided (or PDB assigned) Chain ID.
  • _atom_site.label_entity_id - a unique identifier of all unique polymer and non-polymer molecules in the structure as it is referred to in the _entity category.
  • _atom_site.label_comp_id - PDB assigned residue name.
  • _atom_site.auth_comp_id - author provided or PDB assigned residue name.
  • _atom_site.label_seq_id - unique and sequential residue number (starting from 1 including unmodeled residues) in the polymer sequence.
  • _atom_site.auth_seq_id - author provided residue number.

Example:

loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . MET A 1 1 ? 10.121 49.201 18.054 1.00 88.02 ? 40 MET A N 1
ATOM 2 C CA . MET A 1 1 ? 8.837 48.574 18.359 1.00 85.54 ? 40 MET A CA 1
ATOM 3 C C . MET A 1 1 ? 7.968 48.387 17.110 1.00 78.31 ? 40 MET A C 1
ATOM 4 O O . MET A 1 1 ? 6.906 47.764 17.17 1.00 77.36 ? 40 MET A O 1
ATOM 5 C CB . MET A 1 1 ? 8.081 49.393 19.407 1.00 91.19 ? 40 MET A CB 1
ATOM 6 C CG . MET A 1 1 ? 8.647 49.264 20.815 1.00 97.92 ? 40 MET A CG 1
ATOM 7 S SD . MET A 1 1 ? 8.520 47.577 21.459 1.00 99.09 ? 40 MET A SD 1
ATOM 8 C CE . MET A 1 1 ? 10.226 47.245 21.909 1.00 96.88 ? 40 MET A CE 1
ATOM 9 N N . GLY A 1 2 ? 8.409 48.936 15.983 1.00 64.64 ? 41 GLY A N 1
ATOM 10 C CA . GLY A 1 2 ? 7.802 48.609 14.715 1.00 44.08 ? 41 GLY A CA 1
ATOM 11 C C . GLY A 1 2 ? 8.184 47.194 14.310 1.00 37.87 ? 41 GLY A C 1
ATOM 12 O O . GLY A 1 2 ? 8.744 46.415 15.082 1.00 32.33 ? 41 GLY A O 1
ATOM 13 N N . LEU A 1 3 ? 7.868 46.866 13.059 1.00 29.81 ? 42 LEU A N 1
ATOM 14 C CA . LEU A 1 3 ? 8.194 45.563 12.503 1.00 26.22 ? 42 LEU A CA 1
..... (truncated for brevity)
HETATM 7475 O O1 . GOL F 3 . ? 12.399 17.309 2.493 1.00 49.81 ? 302 GOL A O1 1
HETATM 7476 C C2 . GOL F 3 . ? 11.119 19.504 2.235 1.00 58.42 ? 302 GOL A C2 1
HETATM 7477 O O2 . GOL F 3 . ? 11.275 19.672 0.870 1.00 52.72 ? 302 GOL A O2 1
HETATM 7478 C C3 . GOL F 3 . ? 11.147 20.886 2.974 1.00 60.69 ? 302 GOL A C3 1
HETATM 7479 O O3 . GOL F 3 . ? 11.560 21.902 2.108 1.00 56.04 ? 302 GOL A O3 1
..... (truncated for brevity)
HETATM 7536 O O . HOH P 5 . ? -0.397 5.714 -2.954 1.00 55.09 ? 401 HOH A O 1
HETATM 7537 O O . HOH P 5 . ? 1.933 22.895 0.037 1.00 41.11 ? 402 HOH A O 1
HETATM 7538 O O . HOH P 5 . ? 18.942 20.641 12.691 1.00 35.07 ? 403 HOH A O 1
HETATM 7539 O O . HOH P 5 . ? -0.984 8.117 1.053 1.00 44.71 ? 404 HOH A O 1
HETATM 7540 O O . HOH P 5 . ? -0.000 -0.000 -4.882 0.50 38.73 ? 405 HOH A O 1
HETATM 7541 O O . HOH P 5 . ? 6.821 7.758 19.352 1.00 65.84 ? 406 HOH A O 1
HETATM 7542 O O . HOH P 5 . ? 6.505 18.912 6.900 1.00 43.17 ? 407 HOH A O 1
HETATM 7543 O O . HOH P 5 . ? -4.255 12.564 -7.163 1.00 53.88 ? 408 HOH A O 1
PDBx/mmCIF category Legacy PDB format records Description
_atom_site_anisotrop ANISOU Details about the anisotropic displacement parameters.

Notes:

  • Represent elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as:
    • T = exp{-2 pi2 sumi[sumj(Uij hi hj ai* aj*)]}
    • h = the Miller indices
    • a* = the reciprocal space cell lengths
  • In the legacy PDB format files the same anisotropic temperature factors are scaled by a factor of 104 (Angstroms2) and are presented as integers.

Example:

loop_
_atom_site_anisotrop.id
_atom_site_anisotrop.type_symbol
_atom_site_anisotrop.pdbx_label_atom_id
_atom_site_anisotrop.pdbx_label_alt_id
_atom_site_anisotrop.pdbx_label_comp_id
_atom_site_anisotrop.pdbx_label_asym_id
_atom_site_anisotrop.pdbx_label_seq_id
_atom_site_anisotrop.pdbx_PDB_ins_code
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.pdbx_auth_seq_id
_atom_site_anisotrop.pdbx_auth_comp_id
_atom_site_anisotrop.pdbx_auth_asym_id
_atom_site_anisotrop.pdbx_auth_atom_id
1 N N . MET A 1 ? 1.2107 1.0696 1.0693 0.0076 -0.0422 -0.3059 40 MET A N
2 C CA . MET A 1 ? 1.1724 1.0654 1.0125 0.0219 -0.0147 -0.3086 40 MET A CA
3 C C . MET A 1 ? 1.0644 0.9574 0.9537 0.0404 -0.0040 -0.2902 40 MET A C
4 O O . MET A 1 ? 1.0413 0.9680 0.9301 0.0495 0.0180 -0.2876 40 MET A O
5 C CB . MET A 1 ? 1.2482 1.1430 1.0736 0.0301 -0.0016 -0.3458 40 MET A CB
6 C CG . MET A 1 ? 1.3496 1.2585 1.1122 0.0134 -0.0061 -0.3622 40 MET A CG
7 S SD . MET A 1 ? 1.3676 1.3267 1.0707 0.0023 0.0074 -0.3342 40 MET A SD
8 C CE . MET A 1 ? 1.3559 1.3081 1.0171 -0.0205 -0.0277 -0.3192 40 MET A CE
9 N N . GLY A 2 ? 0.8894 0.7460 0.8208 0.0436 -0.0202 -0.2751 41 GLY A N
10 C CA . GLY A 2 ? 0.6158 0.4733 0.5858 0.0581 -0.0157 -0.2497 41 GLY A CA
11 C C . GLY A 2 ? 0.5329 0.4169 0.4891 0.0499 -0.0142 -0.2242 41 GLY A C
12 O O . GLY A 2 ? 0.4693 0.3760 0.3830 0.0353 -0.0147 -0.2254 41 GLY A O
..... (truncated for brevity)

MISCELLANEOUS RECORDS

PDBx/mmCIF category Legacy PDB format records Description
_database_2 N/A Records the database identifiers of the structure.

Example:

loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 8GDR pdb_00008gdr 10.2210/pdb8gdr/pdb
WWPDB D_1000272577 ? ?
EMDB EMD-29950 ? ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_database_status N/A Details about the deposition date, deposition and processing wwPDB partner site, status of the model file and associated experimental data in the PDB archive.

Example:

_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 8CQO
_pdbx_database_status.recvd_initial_deposition_date 2023-03-06
_pdbx_database_status.SG_entry N
_pdbx_database_status.deposit_site PDBE
_pdbx_database_status.process_site PDBE
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_database_PDB_obs_spr
  • SPRSDE
  • OBSLTE
Details about the obsolete/superseded PDB entries.

Example:

_pdbx_database_PDB_obs_spr.id SPRSDE
_pdbx_database_PDB_obs_spr.date 1984-07-17
_pdbx_database_PDB_obs_spr.pdb_id 4HHB
_pdbx_database_PDB_obs_spr.replace_pdb_id 1HHB
_pdbx_database_PDB_obs_spr.details ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_database_related REMARK 900 Contains references to entries that are related to the entry.

Example:

loop_
_pdbx_database_related.db_name
_pdbx_database_related.details
_pdbx_database_related.db_id
_pdbx_database_related.content_type
EMDB
;Composite map used in construction of PDB 8GDR - SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10.
;
EMD-29950 'associated EM volume'
EMDB
;Overall map of SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10. Used in construction of composite map EMD-29950.
;
EMD-29975 'consensus EM volume'
EMDB
;Locally refined map of SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10. Used in construction of composite map EMD-29950.
;
EMD-40007 'focused EM volume'
PDB 'Structure of SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10' 8GDR unspecified
PDBx/mmCIF category Legacy PDB format records Description
_database_PDB_caveat CAVEAT Details about the outstanding issues with the structure flagged by the Protein Data Bank.

Example:

loop_
_database_PDB_caveat.id
_database_PDB_caveat.text
1 'THR A 137 HAS WRONG CHIRALITY AT ATOM CB'
2 'THR B 12 HAS WRONG CHIRALITY AT ATOM CB'
3 'THR B 50 HAS WRONG CHIRALITY AT ATOM CB'
4 'ASN C 78 HAS WRONG CHIRALITY AT ATOM CA'
5 'THR C 118 HAS WRONG CHIRALITY AT ATOM CB'
6 'HIS D 2 HAS WRONG CHIRALITY AT ATOM CA'
7 'SER D 72 HAS WRONG CHIRALITY AT ATOM CA'
8 'ASP D 73 HAS WRONG CHIRALITY AT ATOM CA'
9 'LEU D 78 HAS WRONG CHIRALITY AT ATOM CA'
10 'LYS D 144 HAS WRONG CHIRALITY AT ATOM CA'
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_audit_support N/A Details about funding support for the entry.

Example:

_pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)'
_pdbx_audit_support.country 'United States'
_pdbx_audit_support.grant_number 'XXX XXXXXXX'
_pdbx_audit_support.ordinal 1
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_contact_author N/A Details about the name and email address of the principal investigator.

Example:

_pdbx_contact_author.id 2
_pdbx_contact_author.email j.smith@domain.name
_pdbx_contact_author.name_first John
_pdbx_contact_author.name_last Smith
_pdbx_contact_author.name_mi J
_pdbx_contact_author.role 'principal investigator/group leader'
_pdbx_contact_author.identifier_ORCID 0000-000x-xxxx-xxxx

ENTRY REVISION HISTORY

PDBx/mmCIF category Legacy PDB format records Description
_pdbx_audit_revision_history REVDAT Entry file type, major and minor revision version numbers and corresponding revision dates.

Example:

loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2023-09-20
2 'Sturcture model' 1 1 2023-10-04
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_audit_revision_details REVDAT Entry file type, type classification of the revision (initial release, coordinate replacement, obsolete, remediation) and additional details describing the revision.

Notes:

  • Major version revision corresponds to updates to the atomic coordinates, polymer sequence(s), and/or chemical identity of a ligand. All other changes are defined as minor.
  • wwPDB retains all major versions with the latest minor versions of an entry within the PDB archive.

Example:

_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_audit_revision_group REVDAT mmCIF groups affected by revision

Example:

_pdbx_audit_revision_group.ordinal 1
_pdbx_audit_revision_group.revision_ordinal 2
_pdbx_audit_revision_group.data_content_type 'Structure model'
_pdbx_audit_revision_group.group 'Database references'
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_audit_revision_category REVDAT mmCIF categories affected by revision

Example:

loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 2 'Structure model' citation
2 2 'Structure model' citation_author
PDBx/mmCIF category Legacy PDB format records Description
_pdbx_audit_revision_item REVDAT mmCIF category items affected by revision.

Example:

loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 2 'Structure model' '_citation.country'
2 2 'Structure model' '_citation.journal_abbrev'
3 2 'Structure model' '_citation.journal_id_ASTM'
4 2 'Structure model' '_citation.journal_id_CSD
5 2 'Structure model' '_citation.journal_id_ISSN'
6 2 'Structure model' '_citation.journal_volume'
7 2 'Structure model' '_citation.page_first'
8 2 'Structure model' '_citation.page_last'
9 2 'Structure model' '_citation.pdbx_database_id_DOI '
10 2 'Structure model' '_citation.pdbx_database_id_PubMed'
11 2 'Structure model' '_citation.title'
12 2 'Structure model' '_citation.year'