Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.198 

Starting Model: experimental
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Crystal Structures of Eschericia Coli and Salmonella Typhimurium 3- Isopropylmalate Dehydrogenase and Comparison with Their Thermophilic Counterpart from Thermus Thermophilus

Wallon, G.Kryger, G.Lovett, S.T.Oshima, T.Ringe, D.Petsko, G.A.

(1997) J Mol Biol 266: 1016-1031

  • DOI: https://doi.org/10.1006/jmbi.1996.0797
  • Primary Citation of Related Structures:  
    1CM7, 1CNZ, 1WAL

  • PubMed Abstract: 

    The basis of protein stability has been investigated by the structural comparison of themophilic enzymes with their mesophilic counterparts. A number of characteristics have been found that can contribute to the stabilization of thermophilic proteins, but no one is uniquely capable of imparting thermostability. The crystal structure of 3-isopropylmalate dehydrogenase (IPMDH) from the mesophiles Escherichia coli and Salmonella typhimurium have been determined by the method of molecular replacement using the known structure of the homologous Thermus thermophilus enzyme. The structure of the E. coli enzyme was refined at a resolution of 2.1 A to an R-factor of 17.3%, that of the S. typhimurium enzyme at 1.7 A resolution to an R-factor of 19.8%. The three structures were compared to elucidate the basis of the higher thermostability of the T. thermophilus enzyme. A mutant that created a cavity in the hydrophobic core of the thermophilic enzyme was designed to investigate the importance of packing density for thermostability. The structure of this mutant was analyzed. The main stabilizing features in the thermophilic enzyme are an increased number of salt bridges, additional hydrogen bonds, a proportionately larger and more hydrophobic subunit interface, shortened N and C termini and a larger number of proline residues. The mutation in the hydrophobic core of T. thermophilus IPMDH resulted in a cavity of 32 A3, but no significant effect on the activity and thermostability of the mutant was observed.

  • Organizational Affiliation

    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254-9910, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
363Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: LEU B
Find proteins for P37412 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P37412 
Go to UniProtKB:  P37412
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37412
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.76 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.9α = 90
b = 100.8β = 90
c = 109.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description