1V5B

The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans

• PDB DOI: https://doi.org/10.2210/pdb1V5B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Heyndrickxia coagulans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-11-22 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: 2.95 Å
• R-Value Free: 0.290 
• R-Value Work: 0.214 

Starting Model: experimental

Literature

Crystal structure of a highly thermo-stabilized mutant of 3-isopropylmalate dehydrogenase from Bacillus coagulans: An evaluation of local packing density in the hydrophobic core

Fujita, K., Tsuchiya, D., Adachi, W., Suzuki, K., Tsunoda, M., Minami, H., Sekiguchi, T., Kobayashi, N., 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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 318.27 kDa 
• Atom Count: 21,885 
• Modelled Residue Count: 2,853 
• Deposited Residue Count: 2,928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B, C, D, E, F, G, H	366	Heyndrickxia coagulans	Mutation(s): 2  EC: 1.1.1.85
UniProt
Find proteins for P12010 (Heyndrickxia coagulans) Explore P12010  Go to UniProtKB:  P12010

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth C], K [auth H], L [auth H], M [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.290 
• R-Value Work: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.2	α = 90
b = 241.3	β = 90
c = 114.1	γ = 90

Software Package:

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

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: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description