1VLC | pdb_00001vlc

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.226 (DCC)
R-Value Work:
0.188 (Depositor), 0.197 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZ26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.226 (DCC)
R-Value Work: 0.188 (Depositor), 0.197 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

Space Group: P 3 2 1

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

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Entry History

Deposition Data

Released Date: 2004-09-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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
Version 1.5: 2024-05-22
Changes: Data collection

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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.