3CEZ | pdb_00003cez

Crystal structure of methionine-R-sulfoxide reductase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3CEZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-29 Released: 2008-03-18 
• Deposition Author(s): Staker, B., Napuli, A., Nakazawa, S.H., Castaneda, L., Alkafeef, S., Vanvoorhis, W., Stewart, L., Myler, P., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Methionine-R-sulfoxide reductase from Burkholderia pseudomallei.

Staker, B., Napuli, A., Nakazawa, S.H., Castaneda, L., Alkafeef, S., Vanvoorhis, W., Stewart, L., Myler, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.25 kDa 
• Atom Count: 2,271 
• Modeled Residue Count: 260 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine-R-sulfoxide reductase	A, B	164	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: msrB, BURPS1710b_2458 EC: 1.8.4.6 (PDB Primary Data), 1.8.4.12 (UniProt)
UniProt
Find proteins for Q3JRF0 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JRF0  Go to UniProtKB:  Q3JRF0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	D [auth A], F [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.093	α = 87.35
b = 45.782	β = 83.22
c = 45.812	γ = 69.36

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Staker, B., Napuli, A., Nakazawa, S.H., Castaneda, L., Alkafeef, S., Vanvoorhis, W., Stewart, L., Myler, P., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description