crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 at 2.0 A resolution

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.247 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Crystal Structures of the Putative Isocitrate Dehydrogenase fromSulfolobus tokodaiiStrain 7 in the Apo and NADP+-Bound Forms.

Kondo, H.Murakami, M.

(2018) Archaea 2018: 7571984-7571984

  • DOI: https://doi.org/10.1155/2018/7571984
  • Primary Citation of Related Structures:  
    2E0C, 2E5M

  • PubMed Abstract: 

    Isocitrate dehydrogenase is a catabolic enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon Sulfolobus tokodaii was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP + -dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism. The crystal structure of ST2166 was determined at 2.0 Å resolution in the apo form, and then the structure of the crystal soaked with NADP + was also determined at 2.4 Å resolution, which contained NADP + bound at the putative active site. Comparisons between the structures of apo and NADP + -bound forms and NADP-IDHs from other prokaryotes suggest that prokaryotic NADP-IDHs recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure.

  • Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, 464-8602 Nagoya, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
409aa long hypothetical NADP-dependent isocitrate dehydrogenase
A, B
409Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Find proteins for Q96YK6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q96YK6 
Go to UniProtKB:  Q96YK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96YK6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.88α = 90
b = 87.72β = 91.37
c = 75.72γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-10-30 
  • Deposition Author(s): Kouyama, T.

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Refinement description