Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

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Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme.

Nagata, C.Moriyama, H.Tanaka, N.Nakasako, M.Yamamoto, M.Ueki, T.Oshima, T.

(1996) Acta Crystallogr D Biol Crystallogr 52: 623-630

  • DOI: https://doi.org/10.1107/S0907444995016623
  • Primary Citation of Related Structures:  
    1XAA, 1XAB, 1XAC, 1XAD

  • PubMed Abstract: 

    The crystal structures of thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus (10T) and a chimeric enzyme between T. thermophilus and Bacillus subtilus with one point mutation (cS82R), were determined at both 100 and 150 K. At the cryogenic condition, the volume of the unit cell decreased by 5% as a result of a contraction in the solvent region. Although the overall structures of both enzymes at low temperature were the same as that of 10T at room temperature, interactions between two domains and between two subunits in a functional dimer of cS82R were significantly altered. The decrease in the average temperature factor of 10T at low temperature and no significant decrease for cS82R suggested that the structure of the engineered enzyme (cS82R) may have many conformational substates even at low temperature, while the native enzyme (10T) at low temperature has a more definite conformation than that at room temperature. The location of water molecules around the enzyme molecule and the calculation of the radii of gyration suggested that cS82R had a weaker hydration than 10T.

  • Organizational Affiliation

    Department of Life Sciences, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-ISOPROPYLMALATE DEHYDROGENASE345Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q5SIY4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIY4 
Go to UniProtKB:  Q5SIY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIY4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77α = 90
b = 77β = 90
c = 156.4γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
PROCESSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Other