Overview
The SEQADV record identifies conflicts between sequence information in the ATOM records of the PDB entry and the sequence database entry given on DBREF. Please note that these records were designed to identify differences and not errors. No assumption is made as to which database contains the correct data. PDB may include REMARK records in the entry that reflect the depositor's view of which database has the correct sequence.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
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1 - 6 Record name "SEQADV"
8 - 11 IDcode idCode ID code of this entry.
13 - 15 Residue name resName Name of the PDB residue in conflict.
17 Character chainID PDB chain identifier.
19 - 22 Integer seqNum PDB sequence number.
23 AChar iCode PDB insertion code.
25 - 28 LString database Sequence database name.
30 - 38 LString dbIdCode Sequence database accession
number.
40 - 42 Residue name dbRes Sequence database residue name.
44 - 48 Integer dbSeq Sequence database sequence number.
50 - 70 LString conflict Conflict comment.
Details
* For cases where there are gaps in the structure as reflected in missing ATOM records, SEQADV records are produced which reflect the lack of correlation between the chain and the sequence database entry. (Several DBREF records are also produced.) Note that internal structural gaps are represented in SEQADV records, whereas missing N-terminus and C-terminus residues are delineated in REMARK 999 records
* If the missing N-terminus residues were not found in the density map, the PDB will attempt to flag these as SEQADV records. However, we cannot guarantee that they will always be handled uniformly since, in a number of cases, neither PDB nor the depositors are certain where chains start and end.
* In a number of cases, conflicts between the sequences found in PDB entries and in PIR or SWISS-PROT entries have been noted. There are several possible reasons for these conflicts, including natural variants or engineered sequences (mutants), polymorphic sequences, or ambiguous or conflicting experimental results. These discrepancies, which were previously described in REMARK records, are now reported in SEQADV.
* SEQADV describes conflicts between residue sequences given by PDB ATOM/HETATM records and those in the appropriate sequence database entry, such as residues missing due to disorder.
* This record will give a description of the differences between the sequence database entries and complete chains. If a chain is referenced by more than one sequence database entry, as in the case of fused genes, then SEQADV will describe the relationship between each chain segment.
* Some of the possible conflict comments:
Cloning artifact
Conflict
Engineered
Disordered
Gap in PDB entry
Missing from [database name]
Variant
Insertion
Deletion
Microheterogeneity
D-configuration
* When conflicts arise which are not classifiable by these terms, a reference to either a published paper, a PDB entry, or a REMARK within the entry is given. References are given in the form YY-VOL-PAGE-CODEN where YY is year of publication, VOL is the journal volume number, PAGE is the starting page and CODEN is the 4-digit code assigned to journals by PDB and the Cambridge Crystallographic Data Centre (CCDC).
* When reference is made to a PDB entry, then the form is PDB: 1ABC, where 1ABC is the relevant entry ID code.
* Finally, the comment "SEE REMARK 999" is included when the explanation for the conflict is too long to fit the SEQADV record.
* Microheterogeneity is to be represented as a variant with one of the possible residues in the site being selected (arbitrarily) as the primary residue, in which case a SEQADV record must be provided for the alternate residue.
Verification/Validation/Value Authority Control
SEQADV records are automatically generated by the PDB.
Relationships to Other Record Types
SEQADV refers to the sequence as found in the ATOM and HETATM records, and to the sequence database reference found on DBREF.
REMARK 999 contains text explaining discrepancies when the explanation is too lengthy to fit in SEQADV.
Example
1 2 3 4 5 6 7
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SEQADV 1ABC ASN A 100A SWS P10725 ASP 100 1994-300-1200-0070
SEQADV 2ABC ASN A 100A SWS P10725 ASP 100 PDB: 1ABC
SEQADV 3ABC MET A -1 SWS P10725 CLONING ARTIFACT
SEQADV 3ABC GLY A 50 SWS P10725 VAL 50 ENGINEERED