1A05

CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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This is version 1.3 of the entry. See complete history


Literature

Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.

Imada, K.Inagaki, K.Matsunami, H.Kawaguchi, H.Tanaka, H.Tanaka, N.Namba, K.

(1998) Structure 6: 971-982

  • DOI: https://doi.org/10.1016/s0969-2126(98)00099-9
  • Primary Citation of Related Structures:  
    1A05

  • PubMed Abstract: 

    3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding.


  • Organizational Affiliation

    International Institute for Advanced Research, Matsushita Electric Industrial Co., Ltd., Seika, Japan. kimada@npn.jst.go.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-ISOPROPYLMALATE DEHYDROGENASE
A, B
358Acidithiobacillus ferrooxidansMutation(s): 0 
Gene Names: LEUB
EC: 1.1.1.85
UniProt
Find proteins for Q56268 (Acidithiobacillus ferrooxidans)
Explore Q56268 
Go to UniProtKB:  Q56268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56268
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.54α = 90
b = 114.24β = 90
c = 130.89γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Other, Refinement description