2CX9 | pdb_00002cx9

Crystal structure of acyl-CoA dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb2CX9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-06-28 Released: 2005-12-28 
• Deposition Author(s): Murayama, K., Kinebuchi, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Crystal structure of acyl-CoA dehydrogenase

Murayama, K., Kinebuchi, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 166.47 kDa 
• Atom Count: 12,199 
• Modeled Residue Count: 1,540 
• Deposited Residue Count: 1,548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acyl-CoA dehydrogenase	A, B, C, D	387	Thermus thermophilus	Mutation(s): 0  EC: 1.3.99.3
UniProt
Find proteins for Q5SGZ2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SGZ2  Go to UniProtKB:  Q5SGZ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth B], G [auth D], H [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.685	α = 90
b = 88.637	β = 91.15
c = 119.557	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-28 
Deposition Author(s): Murayama, K., Kinebuchi, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-12-25
  Changes: Data collection
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations