6EB4

OhrB (Organic Hydroperoxide Resistance protein) from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb6EB4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-04 Released: 2020-02-05 
• Deposition Author(s): Domingos, R.M., Teixeira, R.D., Alegria, T.G.P., Vieira, P.S., Murakami, M.T., Netto, L.E.S.
• Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Substrate and product-assisted catalysis: molecular aspects behind structural switches along Organic Hydroperoxide Resistance Protein catalytic cycle

Domingos, R.M., Teixeira, R.D., Zeida, A., Agudelo, W.A., Alegria, T.G.P., da Silva Neto, J.F., Vieira, P.S., Murakami, M.T., Farah, C.S., Estrin, D.A., Netto, L.E.S.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c01257

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.84 kDa 
• Atom Count: 4,275 
• Modelled Residue Count: 561 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Organic hydroperoxide resistance protein	A, B, C, D	161	Chromobacterium violaceum	Mutation(s): 0  Gene Names: CBW21_15220
UniProt
Find proteins for Q7NV52 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NV52  Go to UniProtKB:  Q7NV52

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth B], F [auth B], G [auth C], H [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.269	α = 90
b = 87.269	β = 90
c = 178.779	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Domingos, R.M., Teixeira, R.D., Alegria, T.G.P., Vieira, P.S., Murakami, M.T., Netto, L.E.S.

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Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	FAPESP: 2013/07937-8

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2020-05-27
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary