5ENU | pdb_00005enu

Crystal structure of an alkyl hyroperoxide reductase from Burkholderia ambifaria

• PDB DOI: https://doi.org/10.2210/pdb5ENU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-09 Released: 2015-11-25 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an alkyl hyroperoxide reductase from Burkholderia ambifaria

Mayclin, S.J., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 36.06 kDa 
• Atom Count: 2,919 
• Modeled Residue Count: 310 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen	A, B	161	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_1774 EC: 1.11.1.24
UniProt
Find proteins for B1YRI5 (Burkholderia ambifaria (strain MC40-6)) Explore B1YRI5  Go to UniProtKB:  B1YRI5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35ENU

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.34	α = 90
b = 37.01	β = 110.08
c = 75.36	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
ARP	model building
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary