5IDX | pdb_00005idx

Crystal structure of an oxidoreductase from Burkholderia vietnamiensis

• PDB DOI: https://doi.org/10.2210/pdb5IDX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia vietnamiensis G4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-24 Released: 2016-03-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an oxidoreductase from Burkholderia vietnamiensis

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 56.1 kDa 
• Atom Count: 4,238 
• Modeled Residue Count: 524 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	267	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_2377
UniProt
Find proteins for A4JGH3 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JGH3  Go to UniProtKB:  A4JGH3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IDX

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.75	α = 90
b = 110.75	β = 90
c = 110.05	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description