|
|||||||||||||||
|
Title SectionThis section contains records used to describe the experiment and the biological macromolecules present in the entry: HEADER, OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and REMARK records. HEADER HEADEROverviewThe HEADER record uniquely identifies a PDB entry through the idCode field. This record also provides a classification for the entry. Finally, it contains the date the coordinates were deposited at the PDB. Record Format
COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------- 1 - 6 Record name "HEADER" 11 - 50 String(40) classification Classifies the molecule(s) 51 - 59 Date depDate Deposition date. This is the date the coordinates were received by the PDB 63 - 66 IDcode idCode This identifier is unique within the PDBDetails
The verification program checks that the deposition date is a legitimate date and that the ID code is well-formed. PDB coordinate entry ID codes do not begin with 0, as this is used to identify the NOC ("no coordinates) files that are bibliographic only, not structural entries. Relationships to Other Record TypesThe classification found in HEADER also appears in KEYWDS, unabbreviated and in no strict order. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 HEADER MUSCLE PROTEIN 02-JUN-93 1MYS HEADER HYDROLASE (CARBOXYLIC ESTER) 08-APR-93 2PHI HEADER COMPLEX (LECTIN/TRANSFERRIN) 07-JAN-94 1LGB OBSLTEOverviewOBSLTE appears in entries that have been withdrawn from distribution. This record acts as a flag in an entry that has been withdrawn from the PDB's full release. It indicates which, if any, new entries have replaced the withdrawn entry. The format allows for the case of multiple new entries replacing one existing entry. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------------------------------------- 1 - 6 Record name "OBSLTE" 9 - 10 Continuation continuation Allows concatenation of multiple records 12 - 20 Date repDate Date that this entry was replaced. 22 - 25 IDcode idCode ID code of this entry. 32 - 35 IDcode rIdCode ID code of entry that replaced this one. 37 - 40 IDcode rIdCode ID code of entry that replaced this one. 42 - 45 IDcode rIdCode ID code of entry that replaced this one. 47 - 50 IDcode rIdCode ID code of entry that replaced this one. 52 - 55 IDcode rIdCode ID code of entry that replaced this one. 57 - 60 IDcode rIdCode ID code of entry that replaced this one. 62 - 65 IDcode rIdCode ID code of entry that replaced this one. 67 - 70 IDcode rIdCode ID code of entry that replaced this one.Details It is PDB policy that only the primary author who submitted an entry has the authority to obsolete it. All OBSLTE entries are available from the PDB archive. Verification/Validation/Value Authority ControlPDB staff adds this record at the time an entry is removed from release. Relationships to Other Record TypesNone. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 OBSLTE 31-JAN-94 1MBP 2MBP TITLEOverviewThe TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------- 1 - 6 Record name "TITLE " 9 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 70 String title Title of the experiment.Details
- Experiment type. - Description of the mutation. - The fact that only alpha carbon coordinates have been provided in the entry.Verification/Validation/Value Authority Control This record is free text so no verification of format is required. The title is supplied by the depositor, but PDB staff may exercise editorial judgment in consultation with depositors in assigning the title. Relationships to Other Record TypesCOMPND, SOURCE, EXPDTA, and REMARKs provide information that may also be found in TITLE. You may think of the title as describing the experiment, and the compound record as describing the molecule(s). Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 TITLE RHIZOPUSPEPSIN COMPLEXED WITH REDUCED PEPTIDE INHIBITOR TITLE BETA-GLUCOSYLTRANSFERASE, ALPHA CARBON COORDINATES ONLY TITLE NMR STUDY OF OXIDIZED THIOREDOXIN MUTANT (C62A,C69A,C73A) TITLE 2 MINIMIZED AVERAGE STRUCTURE CAVEATOverviewCAVEAT warns of chirality errors in an entry. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------- 1 - 6 Record name "CAVEAT" 9 - 10 Continuation continuation Allows concatenation of multiple records. 12 - 15 IDcode idCode PDB ID code of this entry. 20 - 70 String comment Free text giving the reason for the CAVEAT.Details
CAVEAT will be added by the PDB to entries known to be incorrect. COMPNDOverviewThe COMPND record describes the macromolecular contents of an entry. Each macromolecule found in the entry is described by a set of token: value pairs, and is referred to as a COMPND record component. Since the concept of a molecule is difficult to specify exactly, PDB staff may exercise editorial judgment in consultation with depositors in assigning these names. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------------- 1 - 6 Record name "COMPND" 9 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 70 Specification compound Description of the molecular list components.Details
TOKEN VALUE DEFINITION --------------------------------------------------------------------------------- MOL_ID Numbers each component; also used in SOURCE to associate the information. MOLECULE Name of the macromolecule. CHAIN Comma-separated list of chain identifier(s). FRAGMENT Specifies a domain or region of the molecule. SYNONYM Comma-separated list of synonyms for the MOLECULE. EC The Enzyme Commission number associated with the molecule. If there is more than one EC number, they are presented as a comma-separated list. ENGINEERED Indicates that the molecule was produced using recombinant technology or by purely chemical synthesis. MUTATION Indicates if there is a mutation. OTHER_DETAILS Additional comments.
CHAIN must match the chain identifiers(s) of the molecule(s). EC numbers are also checked Relationships to Other Record TypesIn the case of mutations, the SEQADV records will present differences from the reference molecule. REMARK records may further describe the contents of the entry. Also see verification above. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES COMPND 6 OTHER_DETAILS: DEOXY FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: COWPEA CHLOROTIC MOTTLE VIRUS; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: CCMV; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-(*AP*UP*AP*U)-3'); COMPND 7 CHAIN: D, F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RNA (5'-(*AP*U)-3'); COMPND 11 CHAIN: E; COMPND 12 ENGINEERED: YES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEVAMINE A; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.14, 3.2.1.17; COMPND 5 OTHER_DETAILS: PLANT ENDOCHITINASE/LYSOZYME SOURCEOverviewThe SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "SOURCE" 9 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 70 Specification srcName Identifies the source of the macromolecule in list a token: value format.Details
TOKEN VALUE DEFINITION --------------------------------------------------------------------------------- MOL_ID Numbers each molecule. Same as appears in COMPND SYNTHETIC Indicates a chemically-synthesized source. FRAGMENT A domain or fragment of the molecule may be specified ORGANISM_SCIENTIFIC Scientific name of the organism. ORGANISM_COMMON Common name of the organism. STRAIN Identifies the strain. VARIANT Identifies the variant. CELL_LINE The specific line of cells used in the experiment ATCC American Type Culture Collection tissue culture number ORGAN Organized group of tissues that carries on a specialized function TISSUE Organized group of cells with a common function and structure CELL Identifies the particular cell type ORGANELLE Organized structure within a cell SECRETION Identifies the secretion, such as saliva, urine, or venom, from which the molecule was isolated CELLULAR_LOCATION Identifies the location inside (or outside) the cell. PLASMID Identifies the plasmid containing the gene. GENE Identifies the gene. EXPRESSION_SYSTEM System used to express recombinant macromolecules EXPRESSION_SYSTEM_STRAIN Strain of the organism in which the molecule was expressed EXPRESSION_SYSTEM_VARIANT Variant of the organism used as the expression system EXPRESSION_SYSTEM_CELL_LINE The specific line of cells used as the expression system EXPRESSION_SYSTEM_ATCC_NUMBER Identifies the ATCC number of the expression system EXPRESSION_SYSTEM_ORGAN Specific organ which expressed the molecule. EXPRESSION_SYSTEM_TISSUE Specific tissue which expressed the molecule. EXPRESSION_SYSTEM_CELL Specific cell type which expressed the molecule EXPRESSION_SYSTEM_ORGANELLE Specific organelle which expressed the molecule EXPRESSION_SYSTEM_CELLULAR_LOCATION Identifies the location inside or outside the cell which expressed the molecule. EXPRESSION_SYSTEM_VECTOR_TYPE Identifies the type of vector used, i.e., plasmid, virus, or cosmid. EXPRESSION_SYSTEM_VECTOR Identifies the vector used. EXPRESSION_SYSTEM_PLASMID Plasmid used in the recombinant experiment. EXPRESSION_SYSTEM_GENE Name of the gene used in recombinant experiment. OTHER_DETAILS Used to present information on the source which is not given elsewhere.
- When necessary to fully describe hybrid molecules, tokens may appear more than once for a given MOL_ID. - All relevant token: value pairs that taken together fully describe each fragment are grouped following the appropriate FRAGMENT. - Descriptors relative to the full system appear before the FRAGMENT (see Example 3 below).
- The expression system is described. - The organism and cell location given are for the source of the gene used in the cloning experiment. - Transgenic organisms, such as mouse producing human proteins, are treated as expression systems.
The biological source is compared to that found in the sequence databases. Relationships to Other Record TypesEach macromolecule listed in COMPND must have a corresponding source. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AVIAN SARCOMA VIRUS; SOURCE 3 STRAIN: SCHMIDT-RUPPIN B; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PRC23IN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGAN: HEART; SOURCE 5 TISSUE: MUSCLE SOURCE MOL_ID: 1; SOURCE 2 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 3 EXPRESSION_SYSTEM_STRAIN: BE167; SOURCE 4 FRAGMENT: RESIDUES 1-16; SOURCE 5 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 FRAGMENT: RESIDUES 17-214; SOURCE 8 ORGANISM_SCIENTIFIC: BACILLUS MACERANS KEYWDSOverviewThe KEYWDS record contains a set of terms relevant to the entry. Terms in the KEYWDS record provide a simple means of categorizing entries and may be used to generate index files. This record addresses some of the limitations found in the classification field of the HEADER record. It provides the opportunity to add further annotation to the entry in a concise and computer-searchable fashion. Record Format
COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "KEYWDS" 9 - 10 Continuation continuation Allows concatenation of records if necessary 11 - 70 List keywds Comma-separated list of keywords relevant to the entry.Details
- Functional classification. - Metabolic role. - Known biological or chemical activity. - Structural classification.
Terms used in the KEYWDS record are subject to scientific and editorial review. A list of terms, definitions, and synonyms will be maintained at the PDB. Every attempt will be made to provide some level of consistency with keywords used in other biological databases. Relationships to Other Record TypesHEADER records contain a classification term which must also appear in KEYWDS. Scientific judgment will dictate when terms used in one entry to describe a molecule should be included in other entries with the same or similar molecules. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 KEYWDS LYASE, TRICARBOXYLIC ACID CYCLE, MITOCHONDRION, OXIDATIVE KEYWDS 2 METABOLISM EXPDTAOverviewThe EXPDTA record presents information about the experiment. The EXPDTA record identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Permitted values include:
ELECTRON DIFFRACTION ELECTRON MICROSCOPY CRYO-ELECTRON MICROSCOPY SOLUTION SCATTERING, THEORETICAL MODEL FIBER DIFFRACTION FLUORESCENCE TRANSFER NEUTRON DIFFRACTION NMR (may have a qualifier e.g. number of models see examples below) SOLUTION SCATTERING THEORETICAL MODEL* X-RAY DIFFRACTION
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------- 1 - 6 Record name "EXPDTA" 9 - 10 Continuation continuation Allows concatenation of multiple records 11 - 70 SList technique The experimental technique(s) with optional comment describing the sample or experiment.Details
The verification program checks that the EXPDTA record appears in the entry and that the technique matches one of the allowed values. It also checks that the relevant standard REMARK is added in the case of NMR, fiber, or theoretical modeling studies, and that the correct CRYST1 and SCALE are used in these cases. If an entry contains multiple models, the verification program checks for the correct number of matching MODEL/ENDMDL records. Relationships to Other Record TypesIf the experiment is an NMR, fiber, or theoretical modeling study, this may be stated in the TITLE, and the appropriate EXPDTA and REMARK records should appear. Specific details of the data collection and experiment appear in the REMARKs. In the case of a polycrystalline fiber diffraction study, CRYST1 and SCALE contain the normal unit cell data. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 EXPDTA X-RAY DIFFRACTION EXPDTA NEUTRON DIFFRACTION; X-RAY DIFFRACTION EXPDTA NMR, 32 STRUCTURES EXPDTA NMR, REGULARIZED MEAN STRUCTURE EXPDTA FIBER DIFFRACTION AUTHOROverviewThe AUTHOR record contains the names of the people responsible for the contents of the entry. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------- 1 - 6 Record name "AUTHOR" 9 - 10 Continuation continuation Allows concatenation of multiple records 11 - 70 List authorList List of the author names, separated by commas.Details
- First and middle names are indicated by initials, each followed by a period, and precede the surname. - Only the surname (family or last name) of the author is given in full. - Hyphens can be used if they are part of the author's name. - Apostrophes are allowed in surnames. - Umlauts and other character modifiers are not given.
- There is no space after any initial and its following period. - Blank spaces are used in a name only if properly part of the surname (e.g., J.VAN DORN), or between surname and Junior, II, or III. - Abbreviations that are part of a surname, such as St. or Ste., are followed by a period and a space before the next part of the surname. - Group names used for one or all of the authors should be spelled out in full. - The name of the larger group comes before the name of a subdivision, e.g., University of Somewhere Department of Chemistry. - Line breaks between multiple lines in the author List occur only after a comma. - Personal names are not split across two lines. - Names are given in English if there is an accepted English version; otherwise in the native language, transliterated if necessary. - "ET AL." may be used when all authors are not individually listed.Verification/Validation/Value Authority Control The verification program checks that the authorList field is correctly formatted. It does not perform any spelling checks or name verification. Relationships to Other Record TypesThe format of the names in the AUTHOR record is the same as in JRNL and REMARK 1 references. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 AUTHOR M.B.BERRY,B.MEADOR,T.BILDERBACK,P.LIANG,M.GLASER, AUTHOR 2 G.N.PHILLIPS JUNIOR,T.L.ST. STEVENS REVDATOverviewREVDAT records contain a history of the modifications made to an entry since its release. Record Format
COLUMNS DATA TYPE FIELD DEFINITION -------------------------------------------------------- 1 - 6 Record name "REVDAT" 8 - 10 Integer modNum Modification number. 11 - 12 Continuation continuation Allows concatenation of multiple records 14 - 22 Date modDate Date of modification (or release for new entries). This is not repeated on continuation lines. 24 - 28 String(5) modId Identifies this particular modification. It links to the archive used internally by PDB. This is not repeated on continuation lines 32 Integer modType An integer identifying the type of modification. In case of revisions with more than one possible modType, the highest value applicable will be assigned 40 - 45 LString(6) record Name of the modified record. 47 - 52 LString(6) record Name of the modified record. 54 - 59 LString(6) record Name of the modified record. 61 - 66 LString(6) record Name of the modified record.Details
0 Initial released entry. 1 Miscellaneous - mostly typographical. 2 Modification of a CONECT record. 3 Modification to coordinates or transformations. The modType must be one of the defined types, and the given record type must be valid. If modType is 0, the modId must match the entry's ID code in the HEADER record. Relationships to Other Record TypesREMARK 860 presents the correction or change that is made to an entry. Also, see verification above. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 REVDAT 3 15-OCT-89 1PRC 1 REMARK REVDAT 2 19-APR-89 1PRC 2 CONECT REVDAT 1 09-JAN-89 1PRC 0 SPRSDEOverviewThe SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set. One entry may replace many. It is PDB policy that only the principal investigator of a structure has the authority to withdraw it. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------------- 1 - 6 Record name "SPRSDE" 9 - 10 Continuation continuation Allows for multiple ID codes. 12 - 20 Date sprsdeDate Date this entry superseded the listed entries. This field is not copied on continuations. 22 - 25 IDcode idCode ID code of this entry. This field is not copied on continuations. 32 - 35 IDcode sIdCode ID code of a superseded entry. 37 - 40 IDcode sIdCode ID code of a superseded entry. 42 - 45 IDcode sIdCode ID code of a superseded entry. 47 - 50 IDcode sIdCode ID code of a superseded entry. 52 - 55 IDcode sIdCode ID code of a superseded entry. 57 - 60 IDcode sIdCode ID code of a superseded entry. 62 - 65 IDcode sIdCode ID code of a superseded entry. 67 - 70 IDcode sIdCode ID code of a superseded entry.Details
PDB checks that the superseded entries have actually been withdrawn from release. Relationships to Other Record TypesThe sprsdeDate is usually the date the entry is released, and therefore matches the date in the REVDAT 1 record. The ID code found in the idCode field must be the same as one found in the idCode field of the HEADER record. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 SPRSDE 17-JUL-84 4HHB 1HHB SPRSDE 27-FEB-95 1GDJ 1LH4 2LH4 JRNLOverviewThe JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------- 1 - 6 Record name "JRNL " 13 - 70 LString text See Details below.Details
1. AUTH
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "REMARK" 10 LString(1) "1" 13 - 16 LString(4) "AUTH" Appears on all continuation records 17 - 18 Continuation continuation Allows a long list of authors. 20 - 70 List authorList List of the authors. 2. TITL
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "REMARK" 10 LString(1) "1" 13 - 16 LString(4) "TITL" Appears on all continuation records 17 - 18 Continuation continuation Permits long titles. 20 - 70 LString title Title of the article. 3. EDIT
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "REMARK" 10 LString(1) "1" 13 - 16 LString(4) "TITL" Appears on all continuation records 17 - 18 Continuation continuation Permits long titles. 20 - 70 LString title Title of the article. 4. REF
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(3) "REF" 20 - 34 LString(15) "TO BE PUBLISHED"
COLUMNS DATA TYPE FIELD DEFINITION -------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(3) "REF" 17 - 18 Continuation continuation Allows long publication names. 20 - 47 LString pubName Name of the publication including section or series designation. This is the only field of this sub-record which may be continued on successive sub-records. 50 - 51 LString(2) "V." Appears in the first sub-record only, and only if column 55 is non-blank. 52 - 55 String volume Right-justified blank-filled volume information; appears in the first sub-record only. 57 - 61 String page First page of the article; appears in the first sub-record only. 63 - 66 Integer year Year of publication; first sub-record only. 5. PUBL
Continued lines do not begin with a space.
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "PUBL" 17 - 18 Continuation continuation Allows long publisher and place names. 20 - 70 LString pub City of publication and name of the publisher/institution. 6. REFN
COLUMNS DATA TYPE FIELD ------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "REFN"
COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "REFN" 20 - 23 LString(4) "ASTM" 25 - 30 LString(6) astm ASTM devised coden. 33 - 34 LString(2) country Country of publication code as defined in the OCLC/MARC cataloging format (optional). 36 - 39 LString(4) "ISBN" International Standard Book Number or "ISSN" or International Standard Serial Number. "ESSN" 41 - 65 LString isbn ISSN or ISBN number (final digit may be a letter and may contain one or more dashes).Verification/Validation/Value Authority Control PDB verifies that this record is correctly formatted. Citations appearing in JRNL may not also appear in REMARK 1. Relationships to Other Record TypesThe publication cited as the JRNL record may not be repeated in REMARK 1. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 JRNL AUTH G.FERMI,M.F.PERUTZ,B.SHAANAN,R.FOURME JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT JRNL TITL 2 1.74 A RESOLUTION JRNL REF J.MOL.BIOL. V. 175 159 1984 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836Known Problems
|