1k3h: Difference between revisions

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OCA

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 ==NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii==
-<StructureSection load='1k3h' size='340' side='right' caption='[[1k3h]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1k3h' size='340' side='right'caption='[[1k3h]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k3h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"urobacillus_pasteurii"_miquel_1889 "urobacillus pasteurii" miquel 1889]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K3H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k3h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K3H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k3g|1k3g]], [[1c75|1c75]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3h OCA], [http://pdbe.org/1k3h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k3h RCSB], [http://www.ebi.ac.uk/pdbsum/1k3h PDBsum]</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=1k3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3h OCA], [https://pdbe.org/1k3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k3h RCSB], [https://www.ebi.ac.uk/pdbsum/1k3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3h ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CY553_SPOPA CY553_SPOPA]
 == 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/k3/1k3h_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k3/1k3h_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 17: / Line 20: @@
 </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=1k3h ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaningful NOE data (22.7 per residue), 76 dihedral angles, and 59 pseudocontact shifts. The root mean square deviations from the average structure are 0.25+/-0.07 and 0.59+/-0.13 A for the backbone and all heavy atoms, respectively, and the quality assessment of the structure is satisfactory. The solution structure closely reproduces the fold observed in the crystal structure. The backbone mobility was then investigated through amide (15)N relaxation rate and (15)N-(1)H NOE measurements. The protein is rigid in both the sub-nanosecond and millisecond time scales, probably due to the relatively large heme:number of amino acids ratio. Modeling of eight c-type cytochromes from other Gram-positive bacteria with a high sequence identity (&gt;30 %) to the present cytochrome c(553) was performed. Analysis of consensus features accounts for the relatively low reduction potential as being due to extensive heme hydration and indicates residues 34-35, 44-46, 69-72, and 75 as a conserved hydrophobic patch for the interaction with a protein partner. At variance with mitochondrial c-type cytochrome, this protein does not experience pH-dependent coordination equilibria. The reasons for this difference are analyzed.
-NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.,Banci L, Bertini I, Ciurli S, Dikiy A, Dittmer J, Rosato A, Sciara G, Thompsett AR Chembiochem. 2002 Apr 2;3(4):299-310. PMID:11933230<ref>PMID:11933230</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1k3h" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Cytochrome c|Cytochrome c]]
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Urobacillus pasteurii miquel 1889]]
+[[Category: Large Structures]]
-[[Category: Banci, L]]
+[[Category: Sporosarcina pasteurii]]
-[[Category: Bertini, I]]
+[[Category: Banci L]]
-[[Category: Ciurli, S]]
+[[Category: Bertini I]]
-[[Category: Dikiy, A]]
+[[Category: Ciurli S]]
-[[Category: Dittmer, J]]
+[[Category: Dikiy A]]
-[[Category: Rosato, A]]
+[[Category: Dittmer J]]
-[[Category: Sciara, G]]
+[[Category: Rosato A]]
-[[Category: Thompsett, A R]]
+[[Category: Sciara G]]
-[[Category: Bacillus pasteurii]]
+[[Category: Thompsett AR]]
-[[Category: C-553]]
-[[Category: Cytochrome]]
-[[Category: Electron transfer]]
-[[Category: Electron transport]]
-[[Category: Heme]]