5IDW | pdb_00005idw

Crystal structure of an oxidoreductase from Burkholderia vietnamiensis in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb5IDW/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: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an oxidoreductase from Burkholderia vietnamiensis in complex with NADP

Mayclin, S.J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 51.57 kDa 
• Atom Count: 3,798 
• Modeled Residue Count: 450 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	233	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_3023
UniProt
Find proteins for A4JIB1 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JIB1  Go to UniProtKB:  A4JIB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IDW

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.81	α = 90
b = 49.23	β = 94.99
c = 66.96	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
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