3EIV | pdb_00003eiv

Crystal Structure of Single-stranded DNA-binding protein from Streptomyces coelicolor

• PDB DOI: https://doi.org/10.2210/pdb3EIV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptomyces coelicolor
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2009-09-08 
• Deposition Author(s): Luic, M., Stefanic, Z., Vujaklija, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.259 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Structure of the single-stranded DNA-binding protein from Streptomyces coelicolor.

Stefanic, Z., Vujaklija, D., Luic, M.

(2009) Acta Crystallogr D Biol Crystallogr 65: 974-979

• PubMed: 19690375 
• DOI: https://doi.org/10.1107/S0907444909023634
• Primary Citation Related Structures: 
  3EIV


• PubMed Abstract: 
  

  The crystal structure of the single-stranded DNA-binding protein (SSB) from Streptomyces coelicolor, a filamentous soil bacterium with a complex life cycle and a linear chromosome, has been solved and refined at 2.1 A resolution. The three-dimensional structure shows a common conserved central OB-fold that is found in all structurally determined SSB proteins. However, it shows variations in quaternary structure that have previously only been found in mycobacterial SSBs. The strand involved in the clamp mechanism characteristic of this type of quaternary structure leads to higher stability of the homotetramer. To the best of our knowledge, this is the first X-ray structure of an SSB protein from a member of the genus Streptomyces and it was predicted to be the most stable of the structurally characterized bacterial or human mitochondrial SSBs.

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Organizational Affiliation: 
• Rudjer Bosković Institute, Bijenicka cesta 54, Zagreb, Croatia.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.7 kDa 
• Atom Count: 3,434 
• Modeled Residue Count: 420 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein 2	A, B, C, D	199	Streptomyces coelicolor	Mutation(s): 0
UniProt
Find proteins for Q9X8U3 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9X8U3  Go to UniProtKB:  Q9X8U3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.259 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.454	α = 90
b = 104.788	β = 90
c = 163.306	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
X-GEN	data reduction
X-GEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Luic, M., Stefanic, Z., Vujaklija, D.

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description