1RRO

REFINEMENT OF RECOMBINANT ONCOMODULIN AT 1.30 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refinement of recombinant oncomodulin at 1.30 A resolution.

Ahmed, F.R.Rose, D.R.Evans, S.V.Pippy, M.E.To, R.

(1993) J.Mol.Biol. 230: 1216-1224

  • DOI: 10.1006/jmbi.1993.1237

  • PubMed Abstract: 
  • A refinement of the oncomodulin crystal structure at 1.30 A resolution has been carried out with X-ray data from the recombinant protein. The crystallographic R-factor values are 0.169 for 19,995 reflections in the range 6.0 to 1.30 A, which were use ...

    A refinement of the oncomodulin crystal structure at 1.30 A resolution has been carried out with X-ray data from the recombinant protein. The crystallographic R-factor values are 0.169 for 19,995 reflections in the range 6.0 to 1.30 A, which were used for the restrained least-squares refinement, and 0.176 for 20,186 observed reflections in the range 10.0 to 1.30 A. This high resolution refinement has enabled us to make more definitive statements about the molecular structure than was possible heretofore. The present model includes residues 1 to 108, the two Ca2+ of the CD and EF loops, two intermolecular Ca2+, and 103 water molecules per oncomodulin molecule. The electron density maps indicate disordered orientations for ten residues on the hydrophilic surface of the molecule. The pattern of molecular aggregation via intermolecular Ca2+, which occurs in the native rat oncomodulin structure, is also present in the recombinant oncomodulin structure. The Cys18 side-chain is not in a position that would be easily accessible for molecular dimerization via a disulphide bond. The substitution of Glu59, which is preserved in all the determined species of parvalbumin, by Asp59 in oncomodulin seems to break a stabilizing hydrogen bond in the CD loop and render the main-chain in positions 59 to 60 somewhat unstable. This instability in the CD loop, and the strong tendency of oncomodulin for molecular aggregation via intermolecular Ca2+, appear to be the two outstanding features that may account for oncomodulin's biological peculiarities.


    Related Citations: 
    • The Purification of a Unique Calcium-Binding Protein from Morris Hepatoma 5123 Tc
      Macmanus, J.P.
      (1980) Biochim.Biophys.Acta 621: 296
    • Crystallization and Preliminary Crystallographic Data for Oncomodulin
      Przybylska, M.,Ahmed, F.R.,Birnbaum, G.I.,Rose, D.R.
      (1988) J.Mol.Biol. 199: 393
    • Occurrence of a Low-Molecular-Weight Calcium-Binding Protein in Neoplastic Liver
      Macmanus, J.P.
      (1979) Cancer Res. 39: 3000
    • Structure of Oncomodulin Refined at 1.85 Angstroms Resolution: An Example of Extensive Molecular Aggregation Via Ca2+
      Ahmed, F.R.,Przybylska, M.,Rose, D.R.,Birnbaum, G.I.,Pippy, M.E.,Macmanus, J.P.
      (1990) J.Mol.Biol. 216: 127


    Organizational Affiliation

    Institute for Biological Sciences, National Research Council of Canada, Ottawa.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAT ONCOMODULIN
A
108Rattus norvegicusMutation(s): 0 
Gene Names: Ocm
Find proteins for P02631 (Rattus norvegicus)
Go to UniProtKB:  P02631
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.700α = 90.00
b = 65.120β = 90.00
c = 32.940γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other