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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	F [auth B], G [auth C], H [auth D]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34O5M

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

Entry History 

Deposition Data

• Released Date: 2014-01-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

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