3VKZ

3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at atmospheric pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase

Nagae, T.Kawamura, T.Chavas, L.M.G.Niwa, K.Hasegawa, M.Kato, C.Watanabe, N.

(2012) Acta Crystallogr D Biol Crystallogr 68: 300-309

  • DOI: https://doi.org/10.1107/S0907444912001862
  • Primary Citation of Related Structures:  
    3VKZ, 3VL2, 3VL3, 3VL4, 3VL6, 3VL7

  • PubMed Abstract: 

    Hydrostatic pressure induces structural changes in proteins, including denaturation, the mechanism of which has been attributed to water penetration into the protein interior. In this study, structures of 3-isopropylmalate dehydrogenase (IPMDH) from Shewanella oneidensis MR-1 were determined at about 2 Å resolution under pressures ranging from 0.1 to 650 MPa using a diamond anvil cell (DAC). Although most of the protein cavities are monotonically compressed as the pressure increases, the volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa. In addition, the generation of a new cleft on the molecular surface accompanied by water penetration could also be observed at pressures over 580 MPa. These water-penetration phenomena are considered to be initial steps in the pressure-denaturation process of IPMDH.


  • Organizational Affiliation

    Department of Biotechnology, Graduate School of Engineering, Nagoya University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-isopropylmalate dehydrogenase375Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: leuBSO_4235
EC: 1.1.1.85
UniProt
Find proteins for Q8E9N3 (Shewanella oneidensis (strain MR-1))
Explore Q8E9N3 
Go to UniProtKB:  Q8E9N3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8E9N3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.797α = 90
b = 59.003β = 119.07
c = 76.754γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2016-01-13
    Changes: Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description