5pcy - Revision history

OCA at 12:46, 6 March 2024

OCA — Wed, 06 Mar 2024 12:46:37 GMT

←Older revision		Revision as of 12:46, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5pcy' size='340' side='right'caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5pcy' size='340' side='right'caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lombardy_poplar Lombardy poplar~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5PCY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PCY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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]] 1.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [~~http~~://pdbe.org/5pcy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5pcy ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [https://pdbe.org/5pcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [https://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pcy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PLAS1_POPNI PLAS1_POPNI]] Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.	+	[https://www.uniprot.org/uniprot/PLAS1_POPNI PLAS1_POPNI] Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		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=5pcy 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=5pcy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of poplar plastocyanin in the reduced (CuI) state has been determined and refined, using counter data recorded from crystals at pH 3.8, 4.4, 5.1, 5.9, 7.0 and 7.8 (resolution 1.9 A, 1.9 A, 2.05 A, 1.7 A, 1.8 A and 2.15 A; the final residual R value was 0.15, 0.15, 0.16, 0.17, 0.16 and 0.15, respectively). The molecular and crystal structure of the protein is substantially the same in the reduced state as in the oxidized state. The refinements of the structures of the six forms of the reduced protein could therefore be commenced with a model derived from the known structure of CuII-plastocyanin. The refinements were made by reciprocal space least-squares calculations interspersed with inspections of electron-density difference maps. Precautions were taken to minimize any bias of the results of the refinements in the direction of the starting model. The most significant differences among the structures of the reduced protein at the six pH values, or between them and the structure of the oxidized protein, are concentrated at the Cu site. In the reduced protein at high pH (pH 7.8), the CuI atom is co-ordinated by the N delta(imidazole) atoms of His37 and His87, the S gamma(thiolate) atom of Cys84, and the S delta(thioether) atom of Met92, just as in CuII-plastocyanin. The distorted tetrahedral geometry and the unusually long Cu-S(Met92) bond are retained. The only effects of the change in oxidation state are a lengthening of the two Cu-N(His) bonds by about 0.1 A, and small changes in two bond angles involving the Cu-S(Cys) bond. The high-pH form of reduced plastocyanin accordingly meets all the requirements for efficient electron transfer. As the pH is lowered, the Cu atom and the four Cu-binding protein side-chains appear to undergo small but concerted movements in relation to the rest of the molecule. At low pH (pH 3.8), the CuI atom is trigonally co-ordinated by N delta(His37), S gamma(Cys84) and S delta(Met92). The fourth Cu-ligand bond is broken, the Cu atom making only a van der Waals' contact with the imidazole ring of His87. The trigonal geometry of the Cu atom strongly favours CuI, so that this form of the protein should be redox-inactive. This is known to be the case.(ABSTRACT TRUNCATED AT 400 WORDS)

-	Crystal structure analyses of reduced (CuI) poplar plastocyanin at six pH values.,Guss JM, Harrowell PR, Murata M, Norris VA, Freeman HC J Mol Biol. 1986 Nov 20;192(2):361-87. PMID:3560221<ref>PMID:3560221</ref>	+	==See Also==
-		+	*[[Plastocyanin 3D structures\|Plastocyanin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5pcy" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lombardy poplar~~]]	+	[[Category: Populus nigra]]
-	[[Category: Freeman~~, H C~~]]	+	[[Category: Freeman HC]]
-	[[Category: Guss~~, J M~~]]	+	[[Category: Guss JM]]

OCA at 07:47, 2 September 2020

OCA — Wed, 02 Sep 2020 07:47:19 GMT

←Older revision		Revision as of 07:47, 2 September 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES==		==CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES==
-	<StructureSection load='5pcy' size='340' side='right' caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5pcy' size='340' side='right'caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lombardy_poplar Lombardy poplar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5PCY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lombardy_poplar Lombardy poplar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5PCY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://pdbe.org/5pcy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pcy ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://pdbe.org/5pcy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pcy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/5pcy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/5pcy_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 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lombardy poplar]]		[[Category: Lombardy poplar]]
	[[Category: Freeman, H C]]		[[Category: Freeman, H C]]
	[[Category: Guss, J M]]		[[Category: Guss, J M]]

OCA at 21:05, 5 August 2016

OCA — Fri, 05 Aug 2016 21:05:28 GMT

←Older revision		Revision as of 21:05, 5 August 2016
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES==		==CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES==
	<StructureSection load='5pcy' size='340' side='right' caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5pcy' size='340' side='right' caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Populus_nigra Populus nigra~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PCY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lombardy_poplar Lombardy poplar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PCY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy 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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://pdbe.org/5pcy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pcy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		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=5pcy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		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 5pcy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Populus nigra~~]]	+	[[Category: Lombardy poplar]]
	[[Category: Freeman, H C]]		[[Category: Freeman, H C]]
	[[Category: Guss, J M]]		[[Category: Guss, J M]]

OCA at 21:54, 25 December 2014

OCA — Thu, 25 Dec 2014 21:54:10 GMT

←Older revision		Revision as of 21:54, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PCY FirstGlance]. <br>		<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PCY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy 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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PLAS1_POPNI PLAS1_POPNI]] Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Populus nigra]]		[[Category: Populus nigra]]
-	[[Category: Freeman, H C.]]	+	[[Category: Freeman, H C]]
-	[[Category: Guss, J M.]]	+	[[Category: Guss, J M]]

OCA: Protected "5pcy" [edit=sysop:move=sysop]

OCA — Thu, 05 Jun 2014 07:30:40 GMT

Protected "5pcy" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:30, 5 June 2014

OCA at 07:30, 5 June 2014

OCA — Thu, 05 Jun 2014 07:30:38 GMT

←Older revision		Revision as of 07:30, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES==
-	[[~~Image~~:5pcy.~~png\|left~~\|200px]]	+	<StructureSection load='5pcy' size='340' side='right' caption='[[5pcy]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5pcy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PCY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB], [http://www.ebi.ac.uk/pdbsum/5pcy 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/pc/5pcy_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 ==
		+	The structure of poplar plastocyanin in the reduced (CuI) state has been determined and refined, using counter data recorded from crystals at pH 3.8, 4.4, 5.1, 5.9, 7.0 and 7.8 (resolution 1.9 A, 1.9 A, 2.05 A, 1.7 A, 1.8 A and 2.15 A; the final residual R value was 0.15, 0.15, 0.16, 0.17, 0.16 and 0.15, respectively). The molecular and crystal structure of the protein is substantially the same in the reduced state as in the oxidized state. The refinements of the structures of the six forms of the reduced protein could therefore be commenced with a model derived from the known structure of CuII-plastocyanin. The refinements were made by reciprocal space least-squares calculations interspersed with inspections of electron-density difference maps. Precautions were taken to minimize any bias of the results of the refinements in the direction of the starting model. The most significant differences among the structures of the reduced protein at the six pH values, or between them and the structure of the oxidized protein, are concentrated at the Cu site. In the reduced protein at high pH (pH 7.8), the CuI atom is co-ordinated by the N delta(imidazole) atoms of His37 and His87, the S gamma(thiolate) atom of Cys84, and the S delta(thioether) atom of Met92, just as in CuII-plastocyanin. The distorted tetrahedral geometry and the unusually long Cu-S(Met92) bond are retained. The only effects of the change in oxidation state are a lengthening of the two Cu-N(His) bonds by about 0.1 A, and small changes in two bond angles involving the Cu-S(Cys) bond. The high-pH form of reduced plastocyanin accordingly meets all the requirements for efficient electron transfer. As the pH is lowered, the Cu atom and the four Cu-binding protein side-chains appear to undergo small but concerted movements in relation to the rest of the molecule. At low pH (pH 3.8), the CuI atom is trigonally co-ordinated by N delta(His37), S gamma(Cys84) and S delta(Met92). The fourth Cu-ligand bond is broken, the Cu atom making only a van der Waals' contact with the imidazole ring of His87. The trigonal geometry of the Cu atom strongly favours CuI, so that this form of the protein should be redox-inactive. This is known to be the case.(ABSTRACT TRUNCATED AT 400 WORDS)

-	~~<!--~~	+	Crystal structure analyses of reduced (CuI) poplar plastocyanin at six pH values.,Guss JM, Harrowell PR, Murata M, Norris VA, Freeman HC J Mol Biol. 1986 Nov 20;192(2):361-87. PMID:3560221<ref>PMID:3560221</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_5pcy"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_5pcy\| PDB=5pcy \| SCENE= }}~~	+

-	~~===CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_3560221}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 3560221 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_3560221}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~5PCY is a 1 chain structure of sequence from [http:~~/~~/en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:3560221<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Populus nigra]]		[[Category: Populus nigra]]
	[[Category: Freeman, H C.]]		[[Category: Freeman, H C.]]
	[[Category: Guss, J M.]]		[[Category: Guss, J M.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:02:18 2009''

OCA at 07:02, 18 February 2009

OCA — Wed, 18 Feb 2009 07:02:19 GMT

←Older revision		Revision as of 07:02, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	5PCY is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA].	+	5PCY is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PCY OCA].

	==Reference==		==Reference==
-	~~Crystal structure analyses of reduced (CuI) poplar plastocyanin at six pH values., Guss JM, Harrowell PR, Murata M, Norris VA, Freeman HC, J Mol Biol. 1986 Nov 20;192(2):361-87.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/3560221 3560221]~~	+	<ref group="xtra">PMID:3560221</ref><references group="xtra"/>
	[[Category: Populus nigra]]		[[Category: Populus nigra]]
-	[[Category: Single protein]]
	[[Category: Freeman, H C.]]		[[Category: Freeman, H C.]]
	[[Category: Guss, J M.]]		[[Category: Guss, J M.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:08:~~30 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:02:18 2009''

OCA at 11:08, 3 July 2008

OCA — Thu, 03 Jul 2008 11:08:31 GMT

←Older revision		Revision as of 11:08, 3 July 2008
Line 1:		Line 1:
-	[[Image:5pcy.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:5pcy.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_5pcy\| PDB=5pcy \| SCENE= }}		{{STRUCTURE_5pcy\| PDB=5pcy \| SCENE= }}

-	~~'''~~CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES~~'''~~	+	===CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES===


-	~~==Overview==~~	+	<!--
-	The ~~structure of poplar plastocyanin in the reduced (CuI) state has been determined and refined~~, ~~using counter data recorded from crystals at pH 3.8~~, ~~4.4, 5.1, 5.9, 7.0 and 7.8 (resolution 1.9 A, 1.9 A, 2.05 A, 1.7 A, 1.8 A and 2.15 A;~~ the final residual R value was 0.15, 0.15, 0.16, 0.17, 0.16 and 0.15, respectively). The molecular and crystal structure of the protein is substantially the same in the reduced state as in the oxidized state. The refinements of the structures of the six forms of the reduced protein could therefore be commenced with a model derived from the known structure of CuII-plastocyanin. The refinements were made by reciprocal space least-squares calculations interspersed with inspections of electron-density difference maps. Precautions were taken to ~~minimize any bias of~~ the results of the refinements in the direction of the starting model. The most significant differences among the structures of the reduced protein at the six pH values, or between them and the structure of the oxidized protein, are concentrated at the Cu site. In the reduced protein at high pH (~~pH 7.8), the CuI atom is co-ordinated by the N delta(imidazole) atoms of His37 and His87, the S gamma(thiolate) atom of Cys84, and the S delta(thioether) atom of Met92, just~~ as ~~in CuII-plastocyanin~~. ~~The distorted tetrahedral geometry and the unusually long Cu-S(Met92) bond are retained~~. ~~The only effects of the change in oxidation state are a lengthening of the two Cu-N(His~~) ~~bonds by about 0.1 A~~, ~~and small changes in two bond angles involving the Cu-S(Cys) bond. The high-pH form of reduced plastocyanin accordingly meets all the requirements for efficient electron transfer. As the pH~~ is ~~lowered,~~ the ~~Cu atom and the four Cu-binding protein side-chains appear to undergo small but concerted movements in relation to the rest of the molecule~~. ~~At low pH (pH 3.8), the CuI atom is trigonally co~~-~~ordinated by N delta(His37), S gamma(Cys84) and S delta(Met92). The fourth Cu~~-ligand bond is broken, the Cu atom making only a van der Waals' contact with the imidazole ring of His87. The trigonal geometry of the Cu atom strongly favours CuI, so that this form of the protein should be redox-inactive. This is known to be the case.(ABSTRACT TRUNCATED AT 400 WORDS)	+	The line below this paragraph, {{ABSTRACT_PUBMED_3560221}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 3560221 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_3560221}}

	==About this Structure==		==About this Structure==
Line 24:		Line 28:
	[[Category: Freeman, H C.]]		[[Category: Freeman, H C.]]
	[[Category: Guss, J M.]]		[[Category: Guss, J M.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:36:49 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:08:30 2008''

OCA at 19:36, 4 May 2008

OCA — Sun, 04 May 2008 19:36:50 GMT

←Older revision		Revision as of 19:36, 4 May 2008
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	[[Image:5pcy.jpg\|left\|200px]]		[[Image:5pcy.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 5pcy \|SIZE=350\|CAPTION= <scene name='initialview01'>5pcy</scene>~~, ~~resolution 1~~.~~80Å~~	+	The line below this paragraph, containing "STRUCTURE_5pcy", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=CU:COPPER+(II~~)~~+ION'>CU</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY=~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE=~~	+	-->
-	\|~~DOMAIN~~=	+	{{STRUCTURE_5pcy\| PDB=5pcy \| SCENE= }}
-	\|~~RELATEDENTRY~~=	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB]</span>	+
-	}}	+

	'''CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES'''		'''CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES'''
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	[[Category: Freeman, H C.]]		[[Category: Freeman, H C.]]
	[[Category: Guss, J M.]]		[[Category: Guss, J M.]]
-	~~[[Category: electron transport protein(cuproprotein)]]~~	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:36:49 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:42:04 2008''	+

OCA at 02:42, 31 March 2008

OCA — Mon, 31 Mar 2008 02:42:10 GMT

←Older revision		Revision as of 02:42, 31 March 2008
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	\|PDB= 5pcy \|SIZE=350\|CAPTION= <scene name='initialview01'>5pcy</scene>, resolution 1.80Å		\|PDB= 5pcy \|SIZE=350\|CAPTION= <scene name='initialview01'>5pcy</scene>, resolution 1.80Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=CU:COPPER (II) ION'>CU</scene>	+	\|LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5pcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pcy OCA], [http://www.ebi.ac.uk/pdbsum/5pcy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=5pcy RCSB]</span>
	}}		}}

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	[[Category: Freeman, H C.]]		[[Category: Freeman, H C.]]
	[[Category: Guss, J M.]]		[[Category: Guss, J M.]]
-	[[Category: CU]]
	[[Category: electron transport protein(cuproprotein)]]		[[Category: electron transport protein(cuproprotein)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:12:46 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:42:04 2008''