4XXV | pdb_00004xxv

Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb4XXV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-31 Released: 2015-02-25 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, 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: 79.48 kDa 
• Atom Count: 6,471 
• Modeled Residue Count: 711 
• 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: leuB, BTH_II0674 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	D [auth B], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.35	α = 90
b = 60.9	β = 117.85
c = 105.05	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 2.0: 2023-09-27
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy