1FB5 | pdb_00001fb5

LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.252 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1FB5

This is version 1.4 of the entry. See complete history

Literature

Functional and structural characterization of ovine ornithine transcarbamoylase.

De Gregorio, A.Battistutta, R.Arena, N.Panzalorto, M.Francescato, P.Valentini, G.Bruno, G.Zanotti, G.

(2003) Org Biomol Chem 1: 3178-3185

  • DOI: https://doi.org/10.1039/b304901a
  • Primary Citation Related Structures: 
    1FB5

  • PubMed Abstract: 

    Ornithine transcarbamoylase from ovine liver has been purified to homogeneity. Like all anabolic OTCs, the ovine enzyme is a trimer, constituted by identical subunits of 34 kDa. Sequence analysis of the 54 N-terminal residues of ovine OTC shows a high degree of homology with the human enzyme. The optimum pH and the Michaelis constants for the catalytic reaction were determined. The ovine enzyme is the most thermostable one among mammals OTCs, its critical temperature being 6 degrees C higher than those measured for the other enzymes. The enzyme has been crystallised and the structure determined at 3.5 A resolution. Crystals belong to the cubic P4(3)32 space group, with a = b = c = 184.7 A and a solvent content of about 80%. There is no evidence of any ligand in the active site cavity, indicating that the crystals contain an unliganded or T state of the enzyme. The unliganded OTCase enzyme adopts a trimeric structure which, in the crystal, presents a three-fold axis coincident with the crystallographic one. The conformation of each monomer in the trimer is quite similar to that of the liganded human protein, with the exception of a few loops, directly interacting with the substrate(s), which are able to induce a rearrangement of the quaternary organisation of the trimer, that accounts for the cooperative behaviour of the enzyme following the binding of the substrates.


  • Organizational Affiliation
    • Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, 98166 Messina, Italy.

Macromolecule Content 

  • Total Structure Weight: 36.01 kDa 
  • Atom Count: 2,514 
  • Modeled Residue Count: 320 
  • Deposited Residue Count: 320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ORNITHINE TRANSCARBAMOYLASE320Ovis ariesMutation(s): 0 
EC: 2.1.3.3
UniProt
Find proteins for P84010 (Ovis aries)
Explore P84010 
Go to UniProtKB:  P84010
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84010
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NVA

Query on NVA



Download:Ideal Coordinates CCD File
B [auth A]NORVALINE
C5 H11 N O2
SNDPXSYFESPGGJ-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.252 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.7α = 90
b = 184.7β = 90
c = 184.7γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-03-13
    Changes: Source and taxonomy, Structure summary