1eky - Revision history

OCA at 08:26, 22 May 2024

OCA — Wed, 22 May 2024 08:26:21 GMT

←Older revision		Revision as of 08:26, 22 May 2024
Line 20:		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=1eky ConSurf].		</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=1eky ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.
		+
		+	De novo determination of protein structure by NMR using orientational and long-range order restraints.,Hus JC, Marion D, Blackledge M J Mol Biol. 2000 May 19;298(5):927-36. PMID:10801359<ref>PMID:10801359</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:03, 20 March 2024

OCA — Wed, 20 Mar 2024 10:03:40 GMT

←Older revision		Revision as of 10:03, 20 March 2024
Line 1:		Line 1:

	==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==		==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==
-	<StructureSection load='1eky' size='340' side='right'caption='[[1eky~~]], [[NMR_Ensembles_of_Models \| 32 NMR models~~]]' scene=''>	+	<StructureSection load='1eky' size='340' side='right'caption='[[1eky]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EKY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1nbb\|1nbb]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [https://pdbe.org/1eky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [https://www.ebi.ac.uk/pdbsum/1eky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eky ProSAT]</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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [https://pdbe.org/1eky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [https://www.ebi.ac.uk/pdbsum/1eky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eky ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CYCP_RHOCA CYCP_RHOCA]] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known.	+	[https://www.uniprot.org/uniprot/CYCP_RHOCA CYCP_RHOCA] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		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=1eky ConSurf].		</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=1eky ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.
-
-	De novo determination of protein structure by NMR using orientational and long-range order restraints.,Hus JC, Marion D, Blackledge M J Mol Biol. 2000 May 19;298(5):927-36. PMID:10801359<ref>PMID:10801359</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
-	[[Category: Blackledge, M]]	+	[[Category: Blackledge M]]
-	[[Category: Hus~~, J C~~]]	+	[[Category: Hus JC]]
-	[[Category: Marion, D]]	+	[[Category: Marion D]]
-	~~[[Category: Four helix bundle]]~~	+
-	~~[[Category: Oxygen storage-transport complex~~]]	+

OCA at 09:38, 21 July 2021

OCA — Wed, 21 Jul 2021 09:38:56 GMT

←Older revision		Revision as of 09:38, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1eky' size='340' side='right'caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>		<StructureSection load='1eky' size='340' side='right'caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EKY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EKY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nbb\|1nbb]]</div></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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [~~http~~://pdbe.org/1eky PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1eky PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1eky ProSAT]</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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [https://pdbe.org/1eky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [https://www.ebi.ac.uk/pdbsum/1eky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eky ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CYCP_RHOCA CYCP_RHOCA]] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known.	+	[[https://www.uniprot.org/uniprot/CYCP_RHOCA CYCP_RHOCA]] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:25, 16 October 2019

OCA — Wed, 16 Oct 2019 14:25:14 GMT

←Older revision		Revision as of 14:25, 16 October 2019
Line 1:		Line 1:

	==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==		==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==
-	<StructureSection load='1eky' size='340' side='right' caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>	+	<StructureSection load='1eky' size='340' side='right'caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EKY FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
	[[Category: Blackledge, M]]		[[Category: Blackledge, M]]

OCA at 07:18, 20 December 2017

OCA — Wed, 20 Dec 2017 07:18:01 GMT

←Older revision		Revision as of 07:18, 20 December 2017
Line 1:		Line 1:
		+
	==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==		==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==
	<StructureSection load='1eky' size='340' side='right' caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>		<StructureSection load='1eky' size='340' side='right' caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://pdbe.org/1eky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://pdbe.org/1eky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1eky ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/1eky_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/1eky_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c\|Cytochrome c]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:39, 7 February 2016

OCA — Sun, 07 Feb 2016 17:39:05 GMT

←Older revision		Revision as of 17:39, 7 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1eky ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:42, 10 September 2015

OCA — Thu, 10 Sep 2015 03:42:38 GMT

←Older revision		Revision as of 03:42, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://pdbe.org/1eky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 17:08, 24 December 2014

OCA — Wed, 24 Dec 2014 17:08:27 GMT

←Older revision		Revision as of 17:08, 24 December 2014
Line 7:		Line 7:
	<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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYCP_RHOCA CYCP_RHOCA]] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 00:42, 23 December 2014

OCA — Tue, 23 Dec 2014 00:42:48 GMT

←Older revision		Revision as of 00:42, 23 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EKY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
-	[[Category: Blackledge, M.]]	+	[[Category: Blackledge, M]]
-	[[Category: Hus, J C.]]	+	[[Category: Hus, J C]]
-	[[Category: Marion, D.]]	+	[[Category: Marion, D]]
	[[Category: Four helix bundle]]		[[Category: Four helix bundle]]
	[[Category: Oxygen storage-transport complex]]		[[Category: Oxygen storage-transport complex]]

OCA at 11:27, 24 September 2014

OCA — Wed, 24 Sep 2014 11:27:41 GMT

←Older revision		Revision as of 11:27, 24 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1eky.~~png~~\|~~left~~\|200px]]	+	==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION==
		+	<StructureSection load='1eky' size='340' side='right' caption='[[1eky]], [[NMR_Ensembles_of_Models \| 32 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EKY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nbb\|1nbb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [http://www.ebi.ac.uk/pdbsum/1eky PDBsum]</span></td></tr>
		+	<table>
		+	== 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/ek/1eky_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.

-	~~{{STRUCTURE_1eky\| PDB=1eky \| SCENE= }}~~	+	De novo determination of protein structure by NMR using orientational and long-range order restraints.,Hus JC, Marion D, Blackledge M J Mol Biol. 2000 May 19;298(5):927-36. PMID:10801359<ref>PMID:10801359</ref>

-	~~===MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10801359}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1eky]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c\|Cytochrome c]]		*[[Cytochrome c\|Cytochrome c]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010801359<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
	[[Category: Blackledge, M.]]		[[Category: Blackledge, M.]]