1p7g - Revision history

OCA at 09:38, 16 August 2023

2023-08-16T09:38:41Z

←Older revision		Revision as of 09:38, 16 August 2023
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	<StructureSection load='1p7g' size='340' side='right'caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1p7g' size='340' side='right'caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_51768 Atcc 51768~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1P7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P7G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</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='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1iks\|1iks]]~~</~~div~~><~~/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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [https://pdbe.org/1p7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [https://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [~~http~~://pdbe.org/1p7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SODF_PYRAE SODF_PYRAE]] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/SODF_PYRAE SODF_PYRAE] Destroys superoxide anion 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 51768]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Superoxide dismutase~~]]	+	[[Category: Pyrobaculum aerophilum]]
-	[[Category: Eisenberg, D]]	+	[[Category: Eisenberg D]]
-	[[Category: Lee, S]]	+	[[Category: Lee S]]
-	[[Category: Sawaya~~, M R]]~~	+	[[Category: Sawaya MR]]
-	~~[[Category: Alpha-beta]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:24, 9 December 2020

2020-12-09T07:24:47Z

←Older revision		Revision as of 07:24, 9 December 2020
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	==Crystal structure of superoxide dismutase from Pyrobaculum aerophilum==		==Crystal structure of superoxide dismutase from Pyrobaculum aerophilum==
-	<StructureSection load='1p7g' size='340' side='right' caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1p7g' size='340' side='right'caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1P7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1P7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iks\|1iks]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iks\|1iks]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://pdbe.org/1p7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g 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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://pdbe.org/1p7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1p7g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1p7g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 51768]]		[[Category: Atcc 51768]]
		+	[[Category: Large Structures]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Eisenberg, D]]		[[Category: Eisenberg, D]]

OCA at 07:44, 15 February 2018

2018-02-15T07:44:04Z

←Older revision		Revision as of 07:44, 15 February 2018
Line 1:		Line 1:
		+
	==Crystal structure of superoxide dismutase from Pyrobaculum aerophilum==		==Crystal structure of superoxide dismutase from Pyrobaculum aerophilum==
	<StructureSection load='1p7g' size='340' side='right' caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1p7g' size='340' side='right' caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://pdbe.org/1p7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g 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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://pdbe.org/1p7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/p7/1p7g_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p7/1p7g_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 31:		Line 32:
	</div>		</div>
	<div class="pdbe-citations 1p7g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1p7g" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:59, 9 February 2016

2016-02-09T23:59:27Z

←Older revision		Revision as of 23:59, 9 February 2016
Line 20:		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=1p7g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:20, 11 September 2015

2015-09-11T03:20:55Z

←Older revision		Revision as of 03:20, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1p7g' size='340' side='right' caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1p7g' size='340' side='right' caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrobaculum_aerophilum Pyrobaculum aerophilum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P7G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iks\|1iks]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iks\|1iks]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ~~Pyrobaculum aerophilum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g 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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://pdbe.org/1p7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	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 1p7g" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrobaculum aerophilum~~]]	+	[[Category: Atcc 51768]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Eisenberg, D]]		[[Category: Eisenberg, D]]

OCA at 10:24, 25 December 2014

2014-12-25T10:24:43Z

←Older revision		Revision as of 10:24, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P7G FirstGlance]. <br>		<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P7G FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iks\|1iks]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iks\|1iks]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 Pyrobaculum aerophilum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 Pyrobaculum aerophilum])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g 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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SODF_PYRAE SODF_PYRAE]] Destroys superoxide anion 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]]
Line 37:		Line 39:
	[[Category: Pyrobaculum aerophilum]]		[[Category: Pyrobaculum aerophilum]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
-	[[Category: Eisenberg, D.]]	+	[[Category: Eisenberg, D]]
-	[[Category: Lee, S.]]	+	[[Category: Lee, S]]
-	[[Category: Sawaya, M R.]]	+	[[Category: Sawaya, M R]]
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 23:25, 28 September 2014

2014-09-28T23:25:45Z

←Older revision		Revision as of 23:25, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1p7g.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of superoxide dismutase from Pyrobaculum aerophilum==
		+	<StructureSection load='1p7g' size='340' side='right' caption='[[1p7g]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P7G FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iks\|1iks]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 Pyrobaculum aerophilum])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g 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/p7/1p7g_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 crystal structure of superoxide dismutase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was determined by molecular replacement at 1.8 A resolution. The structure determination was made especially challenging by the large number of molecules (24) in the asymmetric unit, the presence of a pseudo-crystallographic twofold operator close to a twinning operator and the inability to detect twinning by conventional means. Molecular replacement proceeded at low resolution in pseudo (apparent) space group P3(2)12 and was facilitated by examination of the self-rotation function and native Patterson map. Refinement, however, stalled at an R factor of 40% when high-resolution data were included. Expanding to the lower symmetry space group P3(2) decreased R (to 22%) and R(free) (to 26%), but not by as much as expected for the quality of data. Finally, despite the apparent lack of evidence from conventional twinning tests [i.e. plots of the second moment of I and N(Z) distributions], a twinning operator was included in the refinement, lowering R and R(free) to 16.2 and 21.7%, respectively. The early detection of twinning appears to have been masked by a deviation in the expected intensity distribution caused by the presence of non-crystallographic translational symmetry. These findings suggest the importance of testing twinning operators in cases where pseudo-translational symmetry can explain negative results from conventional twinning tests. The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme.

-	~~{{STRUCTURE_1p7g\| PDB=1p7g \| SCENE= }}~~	+	Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning.,Lee S, Sawaya MR, Eisenberg D Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2191-9. Epub 2003, Nov 27. PMID:14646077<ref>PMID:14646077</ref>

-	~~===Crystal structure~~ of ~~superoxide dismutase from Pyrobaculum aerophilum===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14646077}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1p7g]] is a 24 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA].~~	+

	==See Also==		==See Also==
	*[[Superoxide Dismutase\|Superoxide Dismutase]]		*[[Superoxide Dismutase\|Superoxide Dismutase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:014646077<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Pyrobaculum aerophilum]]		[[Category: Pyrobaculum aerophilum]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]

OCA at 15:35, 20 October 2012

2012-10-20T15:35:51Z

←Older revision		Revision as of 15:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1p7g]] is a 24 chain structure ~~of [[Superoxide Dismutase]]~~ with sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA].	+	[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA].

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

OCA: Protected "1p7g" [edit=sysop:move=sysop]

2012-07-26T18:53:09Z

Protected "1p7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:53, 26 July 2012

OCA at 18:53, 26 July 2012

2012-07-26T18:53:07Z

←Older revision		Revision as of 18:53, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1p7g.png\|left\|200px]]		[[Image:1p7g.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1p7g", 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_1p7g\| PDB=1p7g \| SCENE= }}		{{STRUCTURE_1p7g\| PDB=1p7g \| SCENE= }}

	===Crystal structure of superoxide dismutase from Pyrobaculum aerophilum===		===Crystal structure of superoxide dismutase from Pyrobaculum aerophilum===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14646077}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14646077 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14646077}}		{{ABSTRACT_PUBMED_14646077}}

	==About this Structure==		==About this Structure==
-	~~1P7G~~ is a 24 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA].	+	[[1p7g]] is a 24 chain structure of [[Superoxide Dismutase]] with sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA].
		+
		+	==See Also==
		+	*[[Superoxide Dismutase\|Superoxide Dismutase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14646077~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014646077</ref><references group="xtra"/>
	[[Category: Pyrobaculum aerophilum]]		[[Category: Pyrobaculum aerophilum]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
Line 30:		Line 21:
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 13:47:02 2009''~~	+