1s05

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[[Image:1s05.gif|left|200px]]
 
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{{Structure
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==NMR-validated structural model for oxidized R.palustris cytochrome c556==
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|PDB= 1s05 |SIZE=350|CAPTION= <scene name='initialview01'>1s05</scene>
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<StructureSection load='1s05' size='340' side='right'caption='[[1s05]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene>
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<table><tr><td colspan='2'>[[1s05]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S05 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 1 model</td></tr>
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|GENE=
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<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>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s05 OCA], [https://pdbe.org/1s05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s05 RCSB], [https://www.ebi.ac.uk/pdbsum/1s05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s05 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/C556_RHOPA C556_RHOPA] Low-spin monoheme cytochrome c.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s0/1s05_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1s05 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The structure of oxidized Rhodopseudomonas palustris cytochrome c(556) has been modeled after that of high-spin cytochrome c' from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. The two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. In order to validate this modeled structure, several structural restraints were obtained by performing a restricted set of NMR experiments, without performing a complete assignment of the protein signals. The aim was to exploit the special restraints arising from the paramagnetism of the metal ion. A total of 43 residual-dipolar-coupling and 74 pseudocontact-shift restraints, which together sampled all regions of the protein, were used in conjunction with over 40 routinely obtained NOE distance restraints. A calculation procedure was undertaken combining the program MODELLER and the solution structure determination program PARAMAGNETIC DYANA, which includes paramagnetism-based restraints. The directions and magnitude of the magnetic susceptibility anisotropy tensor were also calculated. The approach readily provides useful results, especially for paramagnetic metalloproteins of moderate to large dimensions.
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'''NMR-validated structural model for oxidized R.palustris cytochrome c556'''
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NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556).,Bertini I, Faraone-Mennella J, Gray HB, Luchinat C, Parigi G, Winkler JR J Biol Inorg Chem. 2004 Mar;9(2):224-30. Epub 2004 Jan 20. PMID:14735333<ref>PMID:14735333</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1s05" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The structure of oxidized Rhodopseudomonas palustris cytochrome c(556) has been modeled after that of high-spin cytochrome c' from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. The two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. In order to validate this modeled structure, several structural restraints were obtained by performing a restricted set of NMR experiments, without performing a complete assignment of the protein signals. The aim was to exploit the special restraints arising from the paramagnetism of the metal ion. A total of 43 residual-dipolar-coupling and 74 pseudocontact-shift restraints, which together sampled all regions of the protein, were used in conjunction with over 40 routinely obtained NOE distance restraints. A calculation procedure was undertaken combining the program MODELLER and the solution structure determination program PARAMAGNETIC DYANA, which includes paramagnetism-based restraints. The directions and magnitude of the magnetic susceptibility anisotropy tensor were also calculated. The approach readily provides useful results, especially for paramagnetic metalloproteins of moderate to large dimensions.
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*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1S05 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S05 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556)., Bertini I, Faraone-Mennella J, Gray HB, Luchinat C, Parigi G, Winkler JR, J Biol Inorg Chem. 2004 Mar;9(2):224-30. Epub 2004 Jan 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14735333 14735333]
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[[Category: Rhodopseudomonas palustris]]
[[Category: Rhodopseudomonas palustris]]
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[[Category: Single protein]]
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[[Category: Bertini I]]
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[[Category: Bertini, I.]]
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[[Category: Faraone-Mennella J]]
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[[Category: Faraone-Mennella, J.]]
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[[Category: Gray HB]]
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[[Category: Gray, H B.]]
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[[Category: Luchinat C]]
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[[Category: Luchinat, C.]]
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[[Category: Parigi G]]
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[[Category: Parigi, G.]]
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[[Category: Winkler JR]]
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[[Category: Winkler, J R.]]
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[[Category: HEM]]
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[[Category: this is a model obtained by nmr-restrained modeling and minimization.]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:58:39 2008''
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Current revision

NMR-validated structural model for oxidized R.palustris cytochrome c556

PDB ID 1s05

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