1cdp: Difference between revisions

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-{{Seed}}
-[[Image:1cdp.png|left|200px]]
-<!--
+==RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_1cdp", creates the "Structure Box" on the page.
+<StructureSection load='1cdp' size='340' side='right'caption='[[1cdp]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1cdp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyprinus_carpio Cyprinus carpio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CDP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-{{STRUCTURE_1cdp|  PDB=1cdp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cdp OCA], [https://pdbe.org/1cdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cdp RCSB], [https://www.ebi.ac.uk/pdbsum/1cdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cdp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRVB_CYPCA PRVB_CYPCA] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/1cdp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1cdp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Carp parvalbumin coordinates calcium through one carbonyl oxygen atom and the oxygen-containing side chains of 5 amino acid residues, or 4 residues and a water molecule, in a helix-loop-helix structural motif. Other calcium-binding proteins, including calmodulin and troponin C, also possess this unique calcium-binding design, which is designated EF-hand or calmodulin fold. Parvalbumin has two such sites, labeled CD and EF. Each of the calcium-binding sites of refined structures of proteins belonging to this group has a 7-oxygen coordination sphere except those of the structure of parvalbumin as it was reported in 1975. This structure had been refined at 1.9 A using difference Fourier techniques on film data. The CD site appeared to be 6-coordinate and the EF site 8-coordinate. Results of NMR experiments using 113Cd-substituted parvalbumin, however, indicate that the sites are similar to one another with coordination number greater than 6. To resolve the inconsistency between crystallographic and NMR results, 1.6 A area detector data was collected for native and cadmium-substituted parvalbumin; the structures have been refined to R factors of 18.7% and 16.4%, respectively, with acceptable geometry and low errors in atomic coordinates. Differences between the parvalbumin structure described in 1975 and the present structure are addressed, including the discovery of 7-coordination for both the CD and EF sites.
-===RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION===
+Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution.,Swain AL, Kretsinger RH, Amma EL J Biol Chem. 1989 Oct 5;264(28):16620-8. PMID:2777802<ref>PMID:2777802</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1cdp" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_2777802}}, adds the Publication Abstract to the page
+*[[Parvalbumin|Parvalbumin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 2777802 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_2777802}}
+__TOC__
+</StructureSection>
-==About this Structure==
-CDP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cyprinus_carpio Cyprinus carpio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CDP OCA].
-==Reference==
-Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution., Swain AL, Kretsinger RH, Amma EL, J Biol Chem. 1989 Oct 5;264(28):16620-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2777802 2777802]
 [[Category: Cyprinus carpio]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Amma, E L.]]
+[[Category: Amma EL]]
-[[Category: Kretsinger, R H.]]
+[[Category: Kretsinger RH]]
-[[Category: Swain, A L.]]
+[[Category: Swain AL]]
-[[Category: Calcium binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:36:03 2008''