Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 35421.51 
• Atom Count: 2462 
• Residue Count: 315 
• Unique protein chains: 1

1PVV

Refined Structure of Pyrococcus furiosus Ornithine Carbamoyltransferase at 1.87 A

• DOI: 10.2210/pdb1PVV/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
• Expression System: Saccharomyces cerevisiae


• Deposited: 2003-06-29 Released: 2003-12-09 
• Deposition Author(s): Massant, J., Wouters, J., Glansdorff, N.

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Experimental Data Snapshot

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

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: 14646072 


• 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.

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Organizational Affiliation: 

Department of Microbiology, Vrije Universiteit Brussel, B-1070 Brussels, Belgium. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ornithine carbamoyltransferase	A	315	Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)	Mutation(s): 0  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 184.777	α = 90.00
b = 184.777	β = 90.00
c = 184.777	γ = 90.00

Software Package:

Software Name	Purpose
SHELX	model building
SCALEPACK	data scaling
SHELXL-97	refinement
SHELX	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-29 
• Released Date: 2003-12-09 
• Deposition Author(s): Massant, J., Wouters, J., Glansdorff, N.

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