4XXV

Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb4XXV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-01-31 Released: 2015-02-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.174
R-Value Work: 0.149
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 79.48 kDa
Atom Count: 6,471
Modelled Residue Count: 711
Deposited Residue Count: 726
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B	363	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: leuB, BTH_II0674 EC: 1.1.1.85
UniProt
Find proteins for Q2T7H6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T7H6 Go to UniProtKB: Q2T7H6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2T7H6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B]	D [auth B], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.174
R-Value Work: 0.149
R-Value Observed: 0.149
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.35	α = 90
b = 60.9	β = 117.85
c = 105.05	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-02-25
Type: Initial release
Version 2.0: 2023-09-27
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy

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Help and Resources

4XXV

Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD

Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)