1omd: Difference between revisions

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<StructureSection load='1omd' size='340' side='right'caption='[[1omd]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='1omd' size='340' side='right'caption='[[1omd]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1omd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. 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>
<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>
</td></tr><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>
</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>
<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>
<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>
<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>
</table>
</table>
== Function ==
== Function ==
[[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.  
[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.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:2231727</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1omd" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Parvalbumin|Parvalbumin]]
*[[Parvalbumin|Parvalbumin]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Buffalo rat]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ahmed, F R]]
[[Category: Rattus norvegicus]]
[[Category: Birnbaum, G I]]
[[Category: Ahmed FR]]
[[Category: Macmanus, J P]]
[[Category: Birnbaum GI]]
[[Category: Pippy, M E]]
[[Category: Macmanus JP]]
[[Category: Przybylska, M]]
[[Category: Pippy ME]]
[[Category: Rose, D R]]
[[Category: Przybylska M]]
[[Category: Calcium binding protein]]
[[Category: Rose DR]]

Latest revision as of 11:01, 14 February 2024

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

Structural highlights

1omd is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ONCO_RAT Has some calmodulin-like activity with respect to enzyme activation and growth regulation. Binds two calcium ions.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1omd, resolution 1.85Å

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