4IWH | pdb_00004iwh

Crystal structure of a 3-isopropylmalate dehydrogenase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb4IWH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-23 Released: 2013-02-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a 3-isopropylmalate dehydrogenase from Burkholderia pseudomallei

Edwards, T.E., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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: 78.68 kDa 
• Atom Count: 6,208 
• Modeled Residue Count: 713 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B	363	Burkholderia thailandensis E264	Mutation(s): 0  Gene Names: BTH_II0674, leuB EC: 1.1.1.85
UniProt
Find proteins for Q2T7H6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T7H6  Go to UniProtKB:  Q2T7H6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34IWH

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.6	α = 90
b = 60.1	β = 112.86
c = 103.19	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description