1omd

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spinqualitylabelsall models 1omd, resolution 1.85Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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

Overview

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.

About this Structure

1OMD is a Single protein structure of sequence from Rattus norvegicus with CA as ligand. Full crystallographic information is available from OCA.

Reference

Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+., Ahmed FR, Przybylska M, Rose DR, Birnbaum GI, Pippy ME, MacManus JP, J Mol Biol. 1990 Nov 5;216(1):127-40. PMID:2231727

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