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)

Experimental Data Snapshot

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

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1YRI5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

Diffraction Data:

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

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Entry History

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.