2EBA | pdb_00002eba

Crystal structure of the putative glutaryl-CoA dehydrogenase from thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2EBA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-07 Released: 2007-04-01 
• Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.275 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.264 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the putative glutaryl-CoA dehydrogenase from thermus thermophilus

Kumarevel, T.S., Karthe, P., Kuramitsu, S., 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,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 348.96 kDa 
• Atom Count: 24,912 
• Modeled Residue Count: 3,040 
• Deposited Residue Count: 3,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutaryl-CoA dehydrogenase	A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I]	385	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0789 EC: 1.3.99.7 (PDB Primary Data), 1.3.8.6 (UniProt)
UniProt
Find proteins for Q5SK63 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK63  Go to UniProtKB:  Q5SK63

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	I [auth A], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.275 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.264 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.239	α = 75.92
b = 86.239	β = 81.25
c = 157.418	γ = 64.24

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-01 
Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-04-01
  Type: Initial release
  
• Version 1.1: 2007-11-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description