1ls9 - Revision history

OCA at 08:27, 10 April 2024

OCA — Wed, 10 Apr 2024 08:27:11 GMT

←Older revision		Revision as of 08:27, 10 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LS9 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">X-ray diffraction, [[Resolution\|Resolution]] 1.3Å</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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [https://pdbe.org/1ls9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ls9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls9 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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [https://pdbe.org/1ls9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ls9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CYC6_CLAGO CYC6_CLAGO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=1ls9 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=1ls9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	This is a thorough biochemical, spectroscopic, electrochemical, and structural study of a cytochrome c(6) isolated from the filamentous green alga Cladophora glomerata. The protein sequence, elucidated using chemical and mass spectrometric techniques, features 91 amino acids and the characteristic CXXCH heme-binding motif found in c-type cytochromes. The protein is monomeric in both oxidation forms, thereby putting in question a functional role for protein dimerization. Direct electrochemical measurements established, for the first time, the kinetic and thermodynamic data for the redox process in a cytochrome c(6). In particular, the quasi-reversible and diffusion-controlled redox process is accompanied by negative enthalpy and entropy changes, resulting in an E degrees ' value of 0.352 V at 298 K. The pH-dependent properties of the oxidized protein, detected by UV-visible, NMR, and direct cyclic voltammetry, indicate the presence of two acid-base equilibria occurring in the acidic (pK(a) = 4.5) and alkaline regions (pK(a) = 9.0). NMR and electronic spectra allowed the assignment of these equilibria to deprotonation of heme propionate-7 and to replacement of the axial methionine with another ligand, respectively. The 1.3 A resolution X-ray structure of the oxidized protein, revealing a fold typical for class I cytochromes, suggests that the conserved Lys60 replaces the axial methionine at pH >9. The heme solvent accessibility is low, and no water molecules were found in the vicinity of the axial ligands of the heme Fe. A structure-based alignment of cytochromes c(6), and the direct comparison of their structures, indicate a substantial degree of identity between the tertiary structures and suggest patches involved in protein-protein interaction. In particular, the surface electrostatic potential of cytochromes c(6) features a hydrophobic region around the heme cofactor, and a backside surface rich in negative charges.
-
-	Structural basis for the molecular properties of cytochrome c6.,Dikiy A, Carpentier W, Vandenberghe I, Borsari M, Safarov N, Dikaya E, Van Beeumen J, Ciurli S Biochemistry. 2002 Dec 17;41(50):14689-99. PMID:12475218<ref>PMID:12475218</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ls9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Cladophora glomerata]]		[[Category: Cladophora glomerata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carpentier, W]]	+	[[Category: Carpentier W]]
-	~~[[Category: Antiparallel beta-sheet]]~~	+
-	~~[[Category: Cytochrome]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Haem]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Omega loop]]~~	+
-	~~[[Category: Protoporphyrin ix containing fe~~]]	+

OCA at 06:48, 18 August 2021

OCA — Wed, 18 Aug 2021 06:48:40 GMT

←Older revision		Revision as of 06:48, 18 August 2021
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	<StructureSection load='1ls9' size='340' side='right'caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1ls9' size='340' side='right'caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LS9 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='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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [~~http~~://pdbe.org/1ls9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ls9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls9 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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [https://pdbe.org/1ls9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ls9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 12:38, 13 November 2019

OCA — Wed, 13 Nov 2019 12:38:41 GMT

←Older revision		Revision as of 12:38, 13 November 2019
Line 1:		Line 1:

	==Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata==		==Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata==
-	<StructureSection load='1ls9' size='340' side='right' caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='1ls9' size='340' side='right'caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>
Line 26:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1ls9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ls9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Cladophora glomerata]]		[[Category: Cladophora glomerata]]
		+	[[Category: Large Structures]]
	[[Category: Carpentier, W]]		[[Category: Carpentier, W]]
	[[Category: Antiparallel beta-sheet]]		[[Category: Antiparallel beta-sheet]]

OCA at 08:12, 31 January 2018

OCA — Wed, 31 Jan 2018 08:12:42 GMT

←Older revision		Revision as of 08:12, 31 January 2018
Line 1:		Line 1:
		+
	==Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata==		==Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata==
	<StructureSection load='1ls9' size='340' side='right' caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1ls9' size='340' side='right' caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 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"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://pdbe.org/1ls9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://pdbe.org/1ls9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ls/1ls9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ls/1ls9_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 25:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1ls9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ls9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c\|Cytochrome c]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:00, 9 February 2016

OCA — Tue, 09 Feb 2016 23:00:23 GMT

←Older revision		Revision as of 23:00, 9 February 2016
Line 14:		Line 14:
	<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=1ls9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:54, 11 September 2015

OCA — Fri, 11 Sep 2015 02:54:45 GMT

←Older revision		Revision as of 02:54, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 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"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://pdbe.org/1ls9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 1ls9" style="background-color:#fffaf0;"></div>

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

OCA at 10:07, 25 December 2014

OCA — Thu, 25 Dec 2014 10:07:07 GMT

←Older revision		Revision as of 10:07, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Cladophora glomerata]]		[[Category: Cladophora glomerata]]
-	[[Category: Carpentier, W.]]	+	[[Category: Carpentier, W]]
	[[Category: Antiparallel beta-sheet]]		[[Category: Antiparallel beta-sheet]]
	[[Category: Cytochrome]]		[[Category: Cytochrome]]

OCA at 16:18, 28 September 2014

OCA — Sun, 28 Sep 2014 16:18:56 GMT

←Older revision		Revision as of 16:18, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ls9.~~png\|left~~\|200px]]	+	==Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata==
		+	<StructureSection load='1ls9' size='340' side='right' caption='[[1ls9]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LS9 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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ls9 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/ls/1ls9_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 ==
		+	This is a thorough biochemical, spectroscopic, electrochemical, and structural study of a cytochrome c(6) isolated from the filamentous green alga Cladophora glomerata. The protein sequence, elucidated using chemical and mass spectrometric techniques, features 91 amino acids and the characteristic CXXCH heme-binding motif found in c-type cytochromes. The protein is monomeric in both oxidation forms, thereby putting in question a functional role for protein dimerization. Direct electrochemical measurements established, for the first time, the kinetic and thermodynamic data for the redox process in a cytochrome c(6). In particular, the quasi-reversible and diffusion-controlled redox process is accompanied by negative enthalpy and entropy changes, resulting in an E degrees ' value of 0.352 V at 298 K. The pH-dependent properties of the oxidized protein, detected by UV-visible, NMR, and direct cyclic voltammetry, indicate the presence of two acid-base equilibria occurring in the acidic (pK(a) = 4.5) and alkaline regions (pK(a) = 9.0). NMR and electronic spectra allowed the assignment of these equilibria to deprotonation of heme propionate-7 and to replacement of the axial methionine with another ligand, respectively. The 1.3 A resolution X-ray structure of the oxidized protein, revealing a fold typical for class I cytochromes, suggests that the conserved Lys60 replaces the axial methionine at pH >9. The heme solvent accessibility is low, and no water molecules were found in the vicinity of the axial ligands of the heme Fe. A structure-based alignment of cytochromes c(6), and the direct comparison of their structures, indicate a substantial degree of identity between the tertiary structures and suggest patches involved in protein-protein interaction. In particular, the surface electrostatic potential of cytochromes c(6) features a hydrophobic region around the heme cofactor, and a backside surface rich in negative charges.

-	~~{{STRUCTURE_1ls9\| PDB=1ls9 \| SCENE= }}~~	+	Structural basis for the molecular properties of cytochrome c6.,Dikiy A, Carpentier W, Vandenberghe I, Borsari M, Safarov N, Dikaya E, Van Beeumen J, Ciurli S Biochemistry. 2002 Dec 17;41(50):14689-99. PMID:12475218<ref>PMID:12475218</ref>

-	~~===Structure~~ of the ~~Cytochrome c6 from the Green Alga Cladophora glomerata===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12475218}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ls9]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Cladophora_glomerata Cladophora glomerata]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c\|Cytochrome c]]		*[[Cytochrome c\|Cytochrome c]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012475218<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cladophora glomerata]]		[[Category: Cladophora glomerata]]
	[[Category: Carpentier, W.]]		[[Category: Carpentier, W.]]

OCA at 15:26, 20 October 2012

OCA — Sat, 20 Oct 2012 15:26:49 GMT

←Older revision		Revision as of 15:26, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[1ls9]] is a 1 chain structure ~~of [[Cytochrome c]]~~ with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA].	+	[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA].

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

OCA: Protected "1ls9" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 18:24:26 GMT

Protected "1ls9" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:24, 26 July 2012