1omd
From Proteopedia
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|PDB= 1omd |SIZE=350|CAPTION= <scene name='initialview01'>1omd</scene>, resolution 1.85Å | |PDB= 1omd |SIZE=350|CAPTION= <scene name='initialview01'>1omd</scene>, resolution 1.85Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1omd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omd OCA], [http://www.ebi.ac.uk/pdbsum/1omd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1omd RCSB]</span> | ||
}} | }} | ||
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[[Category: Przybylska, M.]] | [[Category: Przybylska, M.]] | ||
[[Category: Rose, D R.]] | [[Category: Rose, D R.]] | ||
| - | [[Category: CA]] | ||
[[Category: calcium binding protein]] | [[Category: calcium binding protein]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:47:19 2008'' |
Revision as of 19:47, 30 March 2008
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| , resolution 1.85Å | |||||||
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| Ligands: | |||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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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