4O5M | pdb_00004o5m

X-ray Crystal Structure of Isovaleryl-CoA Dehydrogenase from Brucella suis

PDB DOI: https://doi.org/10.2210/pdb4O5M/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella suis 1330
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-19 Released: 2014-01-01
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.234 (Depositor), 0.235 (DCC)
R-Value Work:
0.200 (Depositor), 0.202 (DCC)
R-Value Observed:
0.202 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

X-ray Crystal Structure of Isovaleryl-CoA Dehydrogenase from Brucella suis

Fairman, J.W., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 170.56 kDa
Atom Count: 10,541
Modeled Residue Count: 1,412
Deposited Residue Count: 1,560
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isovaleryl-CoA dehydrogenase	A, B, C, D	390	Brucella suis 1330	Mutation(s): 0 Gene Names: ivd, BR0020, BS1330_I0020 EC: 1.3.99.10 (PDB Primary Data), 1.3.8.4 (UniProt)
UniProt
Find proteins for A0A0H3G544 (Brucella suis biovar 1 (strain 1330)) Explore A0A0H3G544 Go to UniProtKB: A0A0H3G544
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3G544
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	F [auth B], G [auth C], H [auth D]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.234 (Depositor), 0.235 (DCC)
R-Value Work: 0.200 (Depositor), 0.202 (DCC)
R-Value Observed: 0.202 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.21	α = 90
b = 91.07	β = 99.25
c = 102.14	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-01

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-01-01
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.