1s05: Difference between revisions
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< | ==NMR-validated structural model for oxidized R.palustris cytochrome c556== | ||
<StructureSection load='1s05' size='340' side='right'caption='[[1s05]]' scene=''> | |||
You may | == Structural highlights == | ||
<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> | |||
</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> | |||
-- | <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=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> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/C556_RHOPA C556_RHOPA] Low-spin monoheme cytochrome c. | |||
== 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/s0/1s05_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=1s05 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1s05" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
< | |||
[[Category: Rhodopseudomonas palustris]] | [[Category: Rhodopseudomonas palustris]] | ||
[[Category: Bertini | [[Category: Bertini I]] | ||
[[Category: Faraone-Mennella | [[Category: Faraone-Mennella J]] | ||
[[Category: Gray | [[Category: Gray HB]] | ||
[[Category: Luchinat | [[Category: Luchinat C]] | ||
[[Category: Parigi | [[Category: Parigi G]] | ||
[[Category: Winkler | [[Category: Winkler JR]] | ||
Latest revision as of 10:26, 9 October 2024
NMR-validated structural model for oxidized R.palustris cytochrome c556NMR-validated structural model for oxidized R.palustris cytochrome c556
Structural highlights
FunctionC556_RHOPA Low-spin monoheme cytochrome c. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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