1PVV

Refined Structure of Pyrococcus furiosus Ornithine Carbamoyltransferase at 1.87 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87 A.

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

(2003) Acta Crystallogr.,Sect.D 59: 2140-2149


  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ornithine carbamoyltransferase
A
315Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Gene Names: argF
EC: 2.1.3.3
Find proteins for Q51742 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q51742
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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 = 90.00
b = 184.777β = 90.00
c = 184.777γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
SCALEPACKdata scaling
SHELXL-97refinement
SHELXphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance