2DHT

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7

• PDB DOI: https://doi.org/10.2210/pdb2DHT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-25 Released: 2007-03-27 
• Deposition Author(s): Kondo, H., Murakami, M., Ihara, K., Suzuki, S., Kouyama, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.272 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Starting Model: experimental

Literature

Crystal structure of isocitrate dehydrogenase of Sulfolobus tokodaii strain7

Kondo, H., Murakami, M., Ihara, K., Suzuki, S., Kouyama, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 93.12 kDa 
• Atom Count: 6,484 
• Modelled Residue Count: 806 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
409aa long hypothetical NADP-dependent isocitrate dehydrogenase	A, B	409	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  EC: 1.1.1.42
UniProt
Find proteins for Q96YK6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96YK6  Go to UniProtKB:  Q96YK6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.272 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.979	α = 90
b = 88.095	β = 91.32
c = 76.216	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
XTALVIEW	refinement
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Kondo, H., Murakami, M., Ihara, K., Suzuki, S., Kouyama, T.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description