5IF3 | pdb_00005if3

Crystal structure of a Short-chain dehydrogenase/reductase SDR from Burkholderia vietnamiensis

• PDB DOI: https://doi.org/10.2210/pdb5IF3/pdb

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


• Deposited: 2016-02-25 Released: 2016-05-04 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Short-chain dehydrogenase/reductase SDR from Burkholderia vietnamiensis

Abendroth, J., Mayclin, S.J., Lorimer, 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: 54.16 kDa 
• Atom Count: 3,355 
• Modeled Residue Count: 425 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	262	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_3729
UniProt
Find proteins for A4JKB1 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JKB1  Go to UniProtKB:  A4JKB1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IF3

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.96	α = 90
b = 85.78	β = 90
c = 128.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description