3m29 - Revision history

OCA at 10:23, 21 February 2024

OCA — Wed, 21 Feb 2024 10:23:35 GMT

←Older revision		Revision as of 10:23, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3m29' size='340' side='right'caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3m29' size='340' side='right'caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M29 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M29 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>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; max-height: 3em;'>[[1dso\|1dso]], [[2v23\|2v23]], [[1dsg\|1dsg]], [[1zby\|1zby]], [[5ccp\|5ccp]], [[3e2n\|3e2n]], [[3e2o\|3e2o]], [[3m23\|3m23]], [[3m25\|3m25]], [[3m26\|3m26]], [[3m27\|3m27]], [[3m28\|3m28]], [[3m2a\|3m2a]], [[3m2b\|3m2b]], [[3m2c\|3m2c]], [[3m2d\|3m2d]], [[3m2e\|3m2e]], [[3m2f\|3m2f]], [[3m2g\|3m2g]], [[3m2h\|3m2h]], [[3m2i\|3m2i]]</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CCP, CCP1, CPO, YKR066C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4932 ATCC 18824])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5]~~ </~~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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [https://pdbe.org/3m29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [https://www.ebi.ac.uk/pdbsum/3m29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m29 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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [https://pdbe.org/3m29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [https://www.ebi.ac.uk/pdbsum/3m29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m29 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== 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=3m29 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=3m29 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The ferryl [Fe(IV)O] intermediate is important in many heme enzymes, and thus, the precise nature of the Fe(IV)-O bond is critical in understanding enzymatic mechanisms. The 1.40 A crystal structure of cytochrome c peroxidase Compound I has been determined as a function of X-ray dose while the visible spectrum was being monitored. The Fe-O bond increases in length from 1.73 A in the low-X-ray dose structure to 1.90 A in the high-dose structure. The low-dose structure correlates well with an Fe(IV) horizontal lineO bond, while we postulate that the high-dose structure is the cryo-trapped Fe(III)-OH species previously thought to be an Fe(IV)-OH species.
-
-	Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.,Meharenna YT, Doukov T, Li H, Soltis SM, Poulos TL Biochemistry. 2010 Apr 13;49(14):2984-6. PMID:20230048<ref>PMID:20230048</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3m29" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]		*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
-	[[Category: Cytochrome-c peroxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Meharenna, Y T~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Poulos, T L~~]]	+	[[Category: Meharenna YT]]
-	[[Category: ~~Heme]]~~	+	[[Category: Poulos TL]]
-	~~[[Category: Hydrogen peroxide]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mitochondrion]]~~	+
-	~~[[Category: Organic radical]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase~~]]	+

OCA at 12:41, 13 October 2021

OCA — Wed, 13 Oct 2021 12:41:48 GMT

←Older revision		Revision as of 12:41, 13 October 2021
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	==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==		==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==
-	<StructureSection load='3m29' size='340' side='right' caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='3m29' size='340' side='right'caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3M29 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M29 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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dso\|1dso]], [[2v23\|2v23]], [[1dsg\|1dsg]], [[1zby\|1zby]], [[5ccp\|5ccp]], [[3e2n\|3e2n]], [[3e2o\|3e2o]], [[3m23\|3m23]], [[3m25\|3m25]], [[3m26\|3m26]], [[3m27\|3m27]], [[3m28\|3m28]], [[3m2a\|3m2a]], [[3m2b\|3m2b]], [[3m2c\|3m2c]], [[3m2d\|3m2d]], [[3m2e\|3m2e]], [[3m2f\|3m2f]], [[3m2g\|3m2g]], [[3m2h\|3m2h]], [[3m2i\|3m2i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dso\|1dso]], [[2v23\|2v23]], [[1dsg\|1dsg]], [[1zby\|1zby]], [[5ccp\|5ccp]], [[3e2n\|3e2n]], [[3e2o\|3e2o]], [[3m23\|3m23]], [[3m25\|3m25]], [[3m26\|3m26]], [[3m27\|3m27]], [[3m28\|3m28]], [[3m2a\|3m2a]], [[3m2b\|3m2b]], [[3m2c\|3m2c]], [[3m2d\|3m2d]], [[3m2e\|3m2e]], [[3m2f\|3m2f]], [[3m2g\|3m2g]], [[3m2h\|3m2h]], [[3m2i\|3m2i]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP, CCP1, CPO, YKR066C ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP, CCP1, CPO, YKR066C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [~~http~~://pdbe.org/3m29 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3m29 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3m29 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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [https://pdbe.org/3m29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [https://www.ebi.ac.uk/pdbsum/3m29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m29 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]	+	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
		+	[[Category: Large Structures]]
	[[Category: Meharenna, Y T]]		[[Category: Meharenna, Y T]]
	[[Category: Poulos, T L]]		[[Category: Poulos, T L]]

OCA at 07:13, 9 January 2019

OCA — Wed, 09 Jan 2019 07:13:56 GMT

←Older revision		Revision as of 07:13, 9 January 2019
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/3m29_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/3m29_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>
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	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Mitochondrion]]		[[Category: Mitochondrion]]
		+	[[Category: Organic radical]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA at 20:23, 4 August 2016

OCA — Thu, 04 Aug 2016 20:23:08 GMT

←Older revision		Revision as of 20:23, 4 August 2016
Line 1:		Line 1:
		+
	==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==		==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==
	<StructureSection load='3m29' size='340' side='right' caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3m29' size='340' side='right' caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M29 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M29 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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dso\|1dso]], [[2v23\|2v23]], [[1dsg\|1dsg]], [[1zby\|1zby]], [[5ccp\|5ccp]], [[3e2n\|3e2n]], [[3e2o\|3e2o]], [[3m23\|3m23]], [[3m25\|3m25]], [[3m26\|3m26]], [[3m27\|3m27]], [[3m28\|3m28]], [[3m2a\|3m2a]], [[3m2b\|3m2b]], [[3m2c\|3m2c]], [[3m2d\|3m2d]], [[3m2e\|3m2e]], [[3m2f\|3m2f]], [[3m2g\|3m2g]], [[3m2h\|3m2h]], [[3m2i\|3m2i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dso\|1dso]], [[2v23\|2v23]], [[1dsg\|1dsg]], [[1zby\|1zby]], [[5ccp\|5ccp]], [[3e2n\|3e2n]], [[3e2o\|3e2o]], [[3m23\|3m23]], [[3m25\|3m25]], [[3m26\|3m26]], [[3m27\|3m27]], [[3m28\|3m28]], [[3m2a\|3m2a]], [[3m2b\|3m2b]], [[3m2c\|3m2c]], [[3m2d\|3m2d]], [[3m2e\|3m2e]], [[3m2f\|3m2f]], [[3m2g\|3m2g]], [[3m2h\|3m2h]], [[3m2i\|3m2i]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP, CCP1, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP, CCP1, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [http://www.ebi.ac.uk/pdbsum/3m29 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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [http://pdbe.org/3m29 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [http://www.ebi.ac.uk/pdbsum/3m29 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m29 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3m29 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3m29" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Meharenna, Y T]]		[[Category: Meharenna, Y T]]
	[[Category: Poulos, T L]]		[[Category: Poulos, T L]]

OCA at 19:17, 24 December 2014

OCA — Wed, 24 Dec 2014 19:17:21 GMT

←Older revision		Revision as of 19:17, 24 December 2014
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	<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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [http://www.ebi.ac.uk/pdbsum/3m29 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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [http://www.ebi.ac.uk/pdbsum/3m29 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:07, 9 December 2014

OCA — Tue, 09 Dec 2014 09:07:06 GMT

←Older revision		Revision as of 09:07, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3m29.~~png~~\|~~left~~\|200px]]	+	==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==
		+	<StructureSection load='3m29' size='340' side='right' caption='[[3m29]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3m29]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M29 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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dso\|1dso]], [[2v23\|2v23]], [[1dsg\|1dsg]], [[1zby\|1zby]], [[5ccp\|5ccp]], [[3e2n\|3e2n]], [[3e2o\|3e2o]], [[3m23\|3m23]], [[3m25\|3m25]], [[3m26\|3m26]], [[3m27\|3m27]], [[3m28\|3m28]], [[3m2a\|3m2a]], [[3m2b\|3m2b]], [[3m2c\|3m2c]], [[3m2d\|3m2d]], [[3m2e\|3m2e]], [[3m2f\|3m2f]], [[3m2g\|3m2g]], [[3m2h\|3m2h]], [[3m2i\|3m2i]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP, CCP1, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=3m29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m29 RCSB], [http://www.ebi.ac.uk/pdbsum/3m29 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/m2/3m29_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 ferryl [Fe(IV)O] intermediate is important in many heme enzymes, and thus, the precise nature of the Fe(IV)-O bond is critical in understanding enzymatic mechanisms. The 1.40 A crystal structure of cytochrome c peroxidase Compound I has been determined as a function of X-ray dose while the visible spectrum was being monitored. The Fe-O bond increases in length from 1.73 A in the low-X-ray dose structure to 1.90 A in the high-dose structure. The low-dose structure correlates well with an Fe(IV) horizontal lineO bond, while we postulate that the high-dose structure is the cryo-trapped Fe(III)-OH species previously thought to be an Fe(IV)-OH species.

-	~~{{STRUCTURE_3m29\| PDB=3m29 \| SCENE= }}~~	+	Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.,Meharenna YT, Doukov T, Li H, Soltis SM, Poulos TL Biochemistry. 2010 Apr 13;49(14):2984-6. PMID:20230048<ref>PMID:20230048</ref>

-	~~===Crystallographic and Single Crystal Spectral Analysis~~ of the ~~Peroxidase Ferryl Intermediate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20230048}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3m29]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020230048<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Meharenna, Y T.]]	+	[[Category: Meharenna, Y T]]
-	[[Category: Poulos, T L.]]	+	[[Category: Poulos, T L]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Hydrogen peroxide]]		[[Category: Hydrogen peroxide]]

OCA at 08:19, 20 October 2012

OCA — Sat, 20 Oct 2012 08:19:14 GMT

←Older revision		Revision as of 08:19, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3m29]] is a 1 chain structure ~~of [[Cytochrome c peroxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA].	+	[[3m29]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA].

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

OCA: Protected "3m29" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 19:09:29 GMT

Protected "3m29" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:09, 25 July 2012

OCA at 19:09, 25 July 2012

OCA — Wed, 25 Jul 2012 19:09:27 GMT

←Older revision		Revision as of 19:09, 25 July 2012
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-	~~{{Seed}}~~	+	[[Image:3m29.png\|left\|200px]]
-	[[Image:3m29.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3m29", 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_3m29\| PDB=3m29 \| SCENE= }}		{{STRUCTURE_3m29\| PDB=3m29 \| SCENE= }}

	===Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate===		===Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20230048}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20230048 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20230048}}		{{ABSTRACT_PUBMED_20230048}}

	==About this Structure==		==About this Structure==
-	~~3M29~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA].	+	[[3m29]] is a 1 chain structure of [[Cytochrome c peroxidase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA].
		+
		+	==See Also==
		+	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20230048~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020230048</ref><references group="xtra"/>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 33:		Line 24:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Mitochondrion]]		[[Category: Mitochondrion]]
-	[[Category: Organic radical]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 12 11:04:40 2010''

OCA at 08:04, 12 May 2010

OCA — Wed, 12 May 2010 08:04:41 GMT

←Older revision		Revision as of 08:04, 12 May 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3m29.jpg\|left\|200px]]

-	The ~~entry 3m29~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3m29", 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_3m29\| PDB=3m29 \| SCENE= }}

-	~~Authors: Meharenna, Y.T., Poulos, T.L.~~	+	===Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate===

-	Description: Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:37:35 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20230048}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20230048 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20230048}}
		+
		+	==About this Structure==
		+	3M29 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M29 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20230048</ref><references group="xtra"/>
		+	[[Category: Cytochrome-c peroxidase]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Meharenna, Y T.]]
		+	[[Category: Poulos, T L.]]
		+	[[Category: Heme]]
		+	[[Category: Hydrogen peroxide]]
		+	[[Category: Iron]]
		+	[[Category: Metal-binding]]
		+	[[Category: Mitochondrion]]
		+	[[Category: Organic radical]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 12 11:04:40 2010''