1V53 | pdb_00001v53

The crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans

• PDB DOI: https://doi.org/10.2210/pdb1V53/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Heyndrickxia coagulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-20 Released: 2005-02-15 
• Deposition Author(s): Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

The crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans

Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

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: 79.51 kDa 
• Atom Count: 5,549 
• Modeled Residue Count: 712 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B	366	Heyndrickxia coagulans	Mutation(s): 0  EC: 1.1.1.85
UniProt
Find proteins for P12010 (Heyndrickxia coagulans) Explore P12010  Go to UniProtKB:  P12010

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.18	α = 90
b = 112.18	β = 90
c = 192.07	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
SCALA	data scaling
AMoRE	phasing
CNS	refinement
d*TREK	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description