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1omd

From Proteopedia

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[[Image:1omd.jpg|left|200px]]
 
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==STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+==
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The line below this paragraph, containing "STRUCTURE_1omd", creates the "Structure Box" on the page.
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<StructureSection load='1omd' size='340' side='right'caption='[[1omd]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1omd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OMD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_1omd| PDB=1omd | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1omd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omd OCA], [https://pdbe.org/1omd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1omd RCSB], [https://www.ebi.ac.uk/pdbsum/1omd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1omd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ONCO_RAT ONCO_RAT] Has some calmodulin-like activity with respect to enzyme activation and growth regulation. Binds two calcium ions.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/1omd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1omd ConSurf].
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<div style="clear:both"></div>
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'''STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+'''
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==See Also==
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*[[Parvalbumin|Parvalbumin]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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==About this Structure==
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1OMD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMD OCA].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/2231727 2231727]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Ahmed FR]]
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[[Category: Ahmed, F R.]]
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[[Category: Birnbaum GI]]
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[[Category: Birnbaum, G I.]]
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[[Category: Macmanus JP]]
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[[Category: Macmanus, J P.]]
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[[Category: Pippy ME]]
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[[Category: Pippy, M E.]]
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[[Category: Przybylska M]]
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[[Category: Przybylska, M.]]
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[[Category: Rose DR]]
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[[Category: Rose, D R.]]
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[[Category: Calcium binding protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:01:39 2008''
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Current revision

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

PDB ID 1omd

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