1VLC

Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VLC/pdb

• Classification: DEHYDROGENASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-20 Released: 2004-09-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 40.74 kDa 
• Atom Count: 2,838 
• Modelled Residue Count: 362 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A	366	Thermotoga maritima	Mutation(s): 0  Gene Names: leuB, TM0556 EC: 1.1.1.85
UniProt
Find proteins for Q9WZ26 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ26  Go to UniProtKB:  Q9WZ26

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 3 2 1
• Diffraction Data: https://doi.org/10.18430/M31VLC

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.78	α = 90
b = 118.78	β = 90
c = 56.699	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	model building
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations