1S3O

Human mitochondrial single strand DNA binding protein (hmSSB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2004) Protein Sci. 13: 1594-1602

  • DOI: 10.1110/ps.04634604

  • PubMed 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, ...

    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.


    Organizational Affiliation

    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, L-448, PO Box 808, Livermore, CA 94551, USA. venclovas@Ilnl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-stranded DNA-binding protein, mitochondrial
A, B
132Homo sapiensMutation(s): 0 
Gene Names: SSBP1 (SSBP)
Find proteins for Q04837 (Homo sapiens)
Go to Gene View: SSBP1
Go to UniProtKB:  Q04837
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.830α = 90.00
b = 51.830β = 90.00
c = 184.240γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
HKL-2000data collection
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance