1upd: Difference between revisions

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-[[Image:1upd.png|left|200px]]
-{{STRUCTURE_1upd|  PDB=1upd  |  SCENE=  }}
+==Oxidized STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6==
+<StructureSection load='1upd' size='340' side='right'caption='[[1upd]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1upd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UPD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</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=1upd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upd OCA], [https://pdbe.org/1upd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1upd RCSB], [https://www.ebi.ac.uk/pdbsum/1upd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1upd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9L915_DESDE Q9L915_DESDE]
+== 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/up/1upd_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/main_output.php?pdb_ID=1upd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using high-resolution X-ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox-Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox-linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redox-cooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox-Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox-linked conformational changes in side-chain residues, results in a significant decrease in the solvent accessibility of hemes I and II.
-===Oxidized STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6===
+Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6.,Bento I, Matias PM, Baptista AM, da Costa PN, van Dongen WM, Saraiva LM, Schneider TR, Soares CM, Carrondo MA Proteins. 2004 Jan 1;54(1):135-52. PMID:14705030<ref>PMID:14705030</ref>
-{{ABSTRACT_PUBMED_14705030}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1upd" style="background-color:#fffaf0;"></div>
-[[1upd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPD OCA].
 ==See Also==
-*[[Cytochrome c|Cytochrome c]]
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:014705030</ref><ref group="xtra">PMID:011551953</ref><ref group="xtra">PMID:007548038</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Desulfovibrio desulfuricans]]
-[[Category: Baptista, A M.]]
+[[Category: Large Structures]]
-[[Category: Bento, I.]]
+[[Category: Baptista AM]]
-[[Category: Carrondo, M A.]]
+[[Category: Bento I]]
-[[Category: Costa, P N.Da.]]
+[[Category: Carrondo MA]]
-[[Category: Dongen, W M.A M.Van.]]
+[[Category: Da Costa PN]]
-[[Category: Matias, P M.]]
+[[Category: Matias PM]]
-[[Category: Saraiva, L M.]]
+[[Category: Saraiva LM]]
-[[Category: Schneider, T R.]]
+[[Category: Schneider TR]]
-[[Category: Soares, C M.]]
+[[Category: Soares CM]]
-[[Category: Electron transport]]
+[[Category: Van Dongen WMAM]]
-[[Category: Tetraheme cytochrome c]]