Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 40539.54 
• Atom Count: 2112 
• Residue Count: 303 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2VW9

Single stranded DNA binding protein complex from Helicobacter pylori

• DOI: 10.2210/pdb2VW9/pdb
• NDB: NA0335

• Classification: DNA BINDING PROTEIN
• Organism(s): Helicobacter pylori (strain ATCC 700392 / 26695)
• Expression System: Escherichia coli


• Deposited: 2008-06-18 Released: 2009-06-02 
• Deposition Author(s): Chan, K.-W., Wang, C.-H., Lee, Y.-J., Sun, Y.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.260 
• R-Value Work: 0.238 

Literature

Single-Stranded DNA-Binding Protein Complex from Helicobacter Pylori Suggests an Ssdna-Binding Surface.

Chan, K.-W., Lee, Y.-J., Wang, C.-H., Huang, H., Sun, Y.-J.

(2009) J.Mol.Biol. 388: 508

• PubMed: 19285993 
• DOI: 10.1016/j.jmb.2009.03.022
• Also Cited By: 3A5U


• PubMed Abstract: 
  

Single-stranded DNA (ssDNA)-binding protein (SSB) plays an important role in DNA replication, recombination, and repair. SSB consists of an N-terminal ssDNA-binding domain with an oligonucleotide/oligosaccharide binding fold and a flexible C-terminal tail involved in protein-protein interactions. SSB from Helicobacter pylori (HpSSB) was isolated, and the ssDNA-binding characteristics of HpSSB were analyzed by fluorescence titration and electrophoretic mobility shift assay. Tryptophan fluorescence quenching was measured as 61%, and the calculated cooperative affinity was 5.4x10(7) M(-1) with an ssDNA-binding length of 25-30 nt. The crystal structure of the C-terminally truncated protein (HpSSBc) in complex with 35-mer ssDNA [HpSSBc-(dT)(35)] was determined at a resolution of 2.3 A. The HpSSBc monomer folds as an oligonucleotide/oligosaccharide binding fold with a Y-shaped conformation. The ssDNA wrapped around the HpSSBc tetramer through a continuous binding path comprising five essential aromatic residues and a positively charged surface formed by numerous basic residues.

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Organizational Affiliation: 

Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SINGLE-STRANDED DNA BINDING PROTEIN	A, B	134	Helicobacter pylori (strain ATCC 700392 / 26695)	Mutation(s): 0  Gene Names: ssb
Find proteins for O25841 (Helicobacter pylori (strain ATCC 700392 / 26695)) Go to UniProtKB:  O25841

Entity ID: 2
Molecule	Chains	Length	Organism
POLY-DT	C	35	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.260 
• R-Value Work: 0.238 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 75.562	α = 90.00
b = 75.562	β = 90.00
c = 117.691	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-18 
• Released Date: 2009-06-02 
• Deposition Author(s): Chan, K.-W., Wang, C.-H., Lee, Y.-J., Sun, Y.-J.

Revision History 

• Version 1.0: 2009-06-02
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance