PDBsum entry 1s3o

DNA binding protein

PDB id: 1s3o

Contents

Protein chains

107 a.a. *

Waters ×21

* Residue conservation analysis

PDB id:

1s3o

Name:

DNA binding protein

Title:

Human mitochondrial single strand DNA binding protein (hmssb)

Structure:

Single-stranded DNA-binding protein, mitochondrial. Chain: a, b. Synonym: mt-ssb, mtssb, pwp1-interacting protein 17

Source:

Homo sapiens. Human. Organism_taxid: 9606

Biol. unit:

Tetramer (from PQS)

Resolution:

2.47Å R-factor: 0.191 R-free: 0.230

Authors:

C.Venclovas,K.Ginalski,C.Kang

Key ref:

C.Venclovas et al. (2004). Sequence-structure mapping errors in the PDB: OB-fold domains. Protein Sci, 13, 1594-1602. PubMed id: 15133161 DOI: 10.1110/ps.04634604

Date:

13-Jan-04 Release date: 22-Jun-04

Protein chains

Q04837  (SSBP_HUMAN) -  Single-stranded DNA-binding protein, mitochondrial from Homo sapiens

Seq: 148 a.a.

Struc: 107 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/ps.04634604

Protein Sci 13:1594-1602 (2004)

PubMed id: 15133161

Sequence-structure mapping errors in the PDB: OB-fold domains.

C.Venclovas, K.Ginalski, C.Kang.

ABSTRACT

The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error-free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure mapping errors. Using energy-based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB-structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence-structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X-ray data for one of the PDB entries containing a fairly inconspicuous sequence-structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions.

Selected figure(s)

Figure 1.
Figure 1. An example of a canonical structure of the OB-fold based on the N-terminal domain of archaeal aspartyl-tRNA synthetase (1b8a [PDB] ; Schmitt et al. 1998). Five -strands (numbered) form a barrel capped with an -helix.

Figure 5.
Figure 5. Structure-based sequence alignment between the two versions of the budding yeast inorganic pyrophosphatase structure: 1pyp [PDB] and a high-resolution structure of the same protein (1e9g [PDB] ). Sequence register errors within 1pyp [PDB] are denoted in bold.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 1594-1602) copyright 2004.

Figures were selected by an automated process.