2BJO | pdb_00002bjo

Crystal Structure of the Organic Hydroperoxide Resistance Protein OhrB of Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2BJO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-02-04 Released: 2006-03-09 
• Deposition Author(s): Cooper, D.R., Surendranath, Y., Bielnicki, J., Devedjiev, Y., Joachimiak, A., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structure of the Bacillus Subtilis Ohrb Hydroperoxide-Resistance Protein in a Fully Oxidized State.

Cooper, D.R., Surendranath, Y., Devedjiev, Y., Bielnicki, J., Derewenda, Z.S.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1269

• PubMed: 18084074 
• DOI: https://doi.org/10.1107/S0907444907050226
• Primary Citation Related Structures: 
  2BJO


• PubMed Abstract: 
  

  The crystal structure of the fully oxidized form of the Bacillus subtilis organic hydroperoxide-resistance (OhrB) protein is reported at 2.1 A resolution. The electron density reveals an intact catalytic disulfide bond (Cys55-Cys119) in each of the two molecules, which are intertwined into a canonical obligate dimer. However, the stereochemistry of the disulfides is unorthodox and strained, suggesting that they are sensitive to reducing agents. A deep solvent-accessible gorge reaching Cys55 may represent the access route for the reductant.

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Organizational Affiliation: 
• Department of Molecular Physiology and Biological Physics, University of Virginia and the PSI2 Integrated Center for Structure-Function Innovation Charlottesville, Virginia 22908, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.89 kDa 
• Atom Count: 2,224 
• Modeled Residue Count: 270 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN OHRB	A, B	136	Bacillus subtilis	Mutation(s): 3
UniProt
Find proteins for P80242 (Bacillus subtilis (strain 168)) Explore P80242  Go to UniProtKB:  P80242

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.34	α = 84.45
b = 41.434	β = 91.51
c = 44.6	γ = 73.89

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-09 
Deposition Author(s): Cooper, D.R., Surendranath, Y., Bielnicki, J., Devedjiev, Y., Joachimiak, A., Derewenda, Z.S.

Revision History  

• Version 1.0: 2006-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary