6EBD

OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) from Chromobacterium violaceum, interacting with dihydrolipoamide

• PDB DOI: https://doi.org/10.2210/pdb6EBD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-08-06 Released: 2020-02-12 
• 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: 2.61 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

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: 68.05 kDa 
• Atom Count: 4,159 
• Modelled Residue Count: 563 
• 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): 1  Gene Names: CBW21_15220
UniProt
Find proteins for A0A202B6V5 (Chromobacterium violaceum) Explore A0A202B6V5  Go to UniProtKB:  A0A202B6V5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J3S	E [auth A], G [auth B], I [auth C]	(6S)-6,8-disulfanyloctanamide C8 H17 N O S2 VLYUGYAKYZETRF-ZETCQYMHSA-N
CL	F [auth A], H [auth B], J [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.675	α = 90
b = 87.675	β = 90
c = 179.609	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: 2020-02-12 
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: 2020-02-12
  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