3cyt: Difference between revisions

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-[[Image:3cyt.png|left|200px]]
+==REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C==
+<StructureSection load='3cyt' size='340' side='right' caption='[[3cyt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3cyt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thunnus_alalunga Thunnus alalunga]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cyt 1cyt]. The December 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Cytochrome c''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_12 10.2210/rcsb_pdb/mom_2002_12]. The May 2007 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aconitase and Iron Regulatory Protein 1''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2007_5 10.2210/rcsb_pdb/mom_2007_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CYT FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
+<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cyt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cyt RCSB], [http://www.ebi.ac.uk/pdbsum/3cyt PDBsum]</span></td></tr>
+<table>
+== 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/cy/3cyt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side.
-{{STRUCTURE_3cyt|  PDB=3cyt  |  SCENE=  }}
+Redox conformation changes in refined tuna cytochrome c.,Takano T, Dickerson RE Proc Natl Acad Sci U S A. 1980 Nov;77(11):6371-5. PMID:6256733<ref>PMID:6256733</ref>
-===REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_6256733}}
-==About this Structure==
-[[3cyt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thunnus_alalunga Thunnus alalunga]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cyt 1cyt]. The December 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Cytochrome c''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_12 10.2210/rcsb_pdb/mom_2002_12]. The May 2007 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aconitase and Iron Regulatory Protein 1''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2007_5 10.2210/rcsb_pdb/mom_2007_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CYT OCA].
 ==See Also==
 *[[Cytochrome c|Cytochrome c]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:006256733</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Aconitase and Iron Regulatory Protein 1]]
 [[Category: Cytochrome c]]