1V5B | pdb_00001v5b

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.290 (Depositor), 0.287 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)

Starting Model: experimental
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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.

Macromolecule Content

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H]	I [auth A], J [auth C], K [auth H], L [auth H], M [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.290 (Depositor), 0.287 (DCC)
R-Value Work: 0.214 (Depositor), 0.215 (DCC)

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

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Entry History

Deposition Data

Released Date: 2005-02-15

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.