Refined Structure of Pyrococcus furiosus Ornithine Carbamoyltransferase at 1.87 A

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 

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This is version 1.3 of the entry. See complete history


Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87 A.

Massant, J.Wouters, J.Glansdorff, N.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2140-2149

  • DOI: https://doi.org/10.1107/s0907444903019231
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Using synchrotron radiation, X-ray data have been collected from Pyrococcus furiosus ornithine carbamoyltransferase (Pfu OTCase) to a maximal resolution of 1.87 A, allowing the refinement of a previous structure at 2.7 A [Villeret et al. (1998), Proc. Natl Acad. Sci. USA, 95, 2801-2806]. Thanks to the high resolution of this refined structure, two sulfate ions and 191 water molecules could be localized directly from the electron-density maps. The identification of these molecules allowed a more rigorous description of the active site and the identification of residues involved in binding carbamoyl phosphate. The improved quality of the model resulted in a better definition of several loops and the various interfaces. The dodecameric protein is composed of four catalytic trimers disposed in a tetrahedral manner. The extreme thermal stability of Pfu OTCase is mainly the result of the strengthening of the intersubunit interactions in a trimer and oligomerization of the trimers into a dodecamer. Interfaces between monomers in a catalytic trimer are characterized by an increase in ion-pair networks compared with mesophilic OTCases. However, the interfaces between catalytic trimers in the dodecameric oligomer are mainly hydrophobic and also involve aromatic-aromatic and cation-pi interactions.

  • Organizational Affiliation

    Department of Microbiology, Vrije Universiteit Brussel, B-1070 Brussels, Belgium. jan.massant@vub.ac.be

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine carbamoyltransferase315Pyrococcus furiosusMutation(s): 0 
Gene Names: ARGF OR PF0594
Find proteins for Q51742 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q51742 
Go to UniProtKB:  Q51742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51742
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.777α = 90
b = 184.777β = 90
c = 184.777γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description