1OMD

STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of oncomodulin refined at 1.85 A 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: 127-140

  • DOI: 10.1016/S0022-2836(05)80065-8
  • Primary Citation of Related Structures:  
    1OMD

  • PubMed Abstract: 
  • The crystal structure of oncomodulin, a 12,000 Mr protein isolated from rat tumours, has been determined by molecular replacement using the carp parvalbumin structure as a starting model. Refinement was performed by cycles of molecular fitting and restrained least-squares, using area-detector intensity data to 1 ...

    The crystal structure of oncomodulin, a 12,000 Mr protein isolated from rat tumours, has been determined by molecular replacement using the carp parvalbumin structure as a starting model. Refinement was performed by cycles of molecular fitting and restrained least-squares, using area-detector intensity data to 1.85 A resolution. For the 5770 reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin molecule. The oncomodulin backbone is closely related to that of parvalbumin; however, some differences are found after a least-squares fit of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2 A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to seven oxygen atoms, including one water molecule. The third Ca2+ is also seven-co-ordinated, to five oxygen atoms belonging to three different oncomodulin molecules and to two water molecules which form hydrogen bonds to a fourth oncomodulin; thus, this intermolecular Ca2+ and its equivalents interlink the molecules into zigzag layers normal to the b axis with a spacing of b/2 or 32.14 A. No such extensive molecular aggregation has been reported for any of the related Ca-binding regulatory proteins of the troponin-C family studied thus far. The Ca-O distances in all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly bound Ca polyhedra.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Data for Oncomodulin
      Przybylska, M., Ahmed, F.R., Birnbaum, G.I., Rose, D.R.
      (1988) J Mol Biol 199: 393
    • A Complete Complementary DNA for the Oncodevelopmental Calcium-Binding Protein, Oncomodulin
      Gillen, M.F., Banville, D., Rutledge, R.G., Narang, S., Seligy, V.L., Whitfield, J.F., Macmanus, J.P.
      (1987) J Biol Chem 262: 5308
    • The Complete Amino Acid Sequence of Oncomodulin-A Parvalbumin-Like Calcium-Binding Protein from Morris Hepatoma 5123Tc
      Macmanus, J.P., Watson, D.C., Yaguchi, M.
      (1983) Eur J Biochem 136: 9

    Organizational Affiliation

    Division of Biological Sciences, National Research Council of Canada, Ottawa.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ONCOMODULIN A108Rattus norvegicusMutation(s): 0 
Gene Names: Ocm
Find proteins for P02631 (Rattus norvegicus)
Explore P02631 
Go to UniProtKB:  P02631
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.59α = 90
b = 64.28β = 90
c = 33.07γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1991-07-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance