1s05

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

1s05 is a 1 chain structure with sequence from Rhodopseudomonas palustris. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 1 model
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C556_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 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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bertini I, Faraone-Mennella J, Gray HB, Luchinat C, Parigi G, Winkler JR. NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556). J Biol Inorg Chem. 2004 Mar;9(2):224-30. Epub 2004 Jan 20. PMID:14735333 doi:http://dx.doi.org/10.1007/s00775-003-0511-2

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1s05"

@@ Line 1: / Line 1: @@
 ==NMR-validated structural model for oxidized R.palustris cytochrome c556==
-<StructureSection load='1s05' size='340' side='right'caption='[[1s05]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1s05' size='340' side='right'caption='[[1s05]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1s05]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodobacillus_palustris"_molisch_1907 "rhodobacillus palustris" molisch 1907]. 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>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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, 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.
+[https://www.uniprot.org/uniprot/C556_RHOPA C556_RHOPA] Low-spin monoheme cytochrome c.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <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/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Rhodobacillus palustris molisch 1907]]
 [[Category: Large Structures]]
-[[Category: Bertini, I]]
+[[Category: Rhodopseudomonas palustris]]
-[[Category: Faraone-Mennella, J]]
+[[Category: Bertini I]]
-[[Category: Gray, H B]]
+[[Category: Faraone-Mennella J]]
-[[Category: Luchinat, C]]
+[[Category: Gray HB]]
-[[Category: Parigi, G]]
+[[Category: Luchinat C]]
-[[Category: Winkler, J R]]
+[[Category: Parigi G]]
-[[Category: Electron transport]]
+[[Category: Winkler JR]]
-[[Category: This is a model obtained by nmr-restrained modeling and minimization]]

1s05

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox