3bnb - Revision history

OCA at 12:11, 30 August 2023

2023-08-30T12:11:04Z

←Older revision		Revision as of 12:11, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3bnb' size='340' side='right'caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='3bnb' size='340' side='right'caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BNB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 1.45Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1f8n\|1f8n]]~~, [[~~3bnc~~\|~~3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>LOX1.1, LOX1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3847 Glycine hispida])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12]~~ </~~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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [https://pdbe.org/3bnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [https://www.ebi.ac.uk/pdbsum/3bnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnb 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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [https://pdbe.org/3bnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [https://www.ebi.ac.uk/pdbsum/3bnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>	+	[https://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~hispida~~]]	+	[[Category: Glycine max]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Oxidoreductase]]~~	+	[[Category: Tomchick DR]]
-	[[Category: Tomchick~~, D R]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Fatty acid biosynthesis]]~~	+
-	~~[[Category: Fatty acid]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Lipid synthesis]]~~	+
-	~~[[Category: Lipoxygenase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Metalloprotein]]~~	+
-	~~[[Category: Oxylipin biosynthesis~~]]	+

OCA at 18:59, 20 October 2021

2021-10-20T18:59:19Z

←Older revision		Revision as of 18:59, 20 October 2021
Line 1:		Line 1:

	==Lipoxygenase-1 (Soybean) I553L Mutant==		==Lipoxygenase-1 (Soybean) I553L Mutant==
-	<StructureSection load='3bnb' size='340' side='right' caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='3bnb' size='340' side='right'caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BNB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [~~http~~://pdbe.org/3bnb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bnb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnb 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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [https://pdbe.org/3bnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [https://www.ebi.ac.uk/pdbsum/3bnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>	+	[[https://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Glycine hispida]]		[[Category: Glycine hispida]]
		+	[[Category: Large Structures]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Tomchick, D R]]		[[Category: Tomchick, D R]]

OCA at 08:01, 31 October 2018

2018-10-31T08:01:07Z

←Older revision		Revision as of 08:01, 31 October 2018
Line 1:		Line 1:
		+
	==Lipoxygenase-1 (Soybean) I553L Mutant==		==Lipoxygenase-1 (Soybean) I553L Mutant==
	<StructureSection load='3bnb' size='340' side='right' caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='3bnb' size='340' side='right' caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://pdbe.org/3bnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb 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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://pdbe.org/3bnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bn/3bnb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bn/3bnb_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>

OCA at 01:40, 10 February 2016

2016-02-10T01:40:56Z

←Older revision		Revision as of 01:40, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3bnb' size='340' side='right' caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='3bnb' size='340' side='right' caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Glycine_max~~ Glycine ~~max~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BNB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine ~~max~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Lipoxygenase Lipoxygenase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb 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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://pdbe.org/3bnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=3bnb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3bnb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~max~~]]	+	[[Category: Glycine hispida]]
-	[[Category: ~~Lipoxygenase~~]]	+	[[Category: Oxidoreductase]]
	[[Category: Tomchick, D R]]		[[Category: Tomchick, D R]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
Line 41:		Line 42:
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Lipid synthesis]]		[[Category: Lipid synthesis]]
		+	[[Category: Lipoxygenase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Metalloprotein]]		[[Category: Metalloprotein]]
-	[[Category: Oxidoreductase]]
	[[Category: Oxylipin biosynthesis]]		[[Category: Oxylipin biosynthesis]]

OCA at 10:55, 25 December 2014

2014-12-25T10:55:15Z

←Older revision		Revision as of 10:55, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BNB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BNB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine max])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine max])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipoxygenase Lipoxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipoxygenase Lipoxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb 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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Glycine max]]		[[Category: Glycine max]]
	[[Category: Lipoxygenase]]		[[Category: Lipoxygenase]]
-	[[Category: Tomchick, D R.]]	+	[[Category: Tomchick, D R]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]
Line 39:		Line 41:
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Lipid synthesis]]		[[Category: Lipid synthesis]]
-	[[Category: Lipoxygenase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Metalloprotein]]		[[Category: Metalloprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Oxylipin biosynthesis]]		[[Category: Oxylipin biosynthesis]]

OCA at 21:17, 2 October 2014

2014-10-02T21:17:08Z

←Older revision		Revision as of 21:17, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3bnb.~~png~~\|~~left~~\|200px]]	+	==Lipoxygenase-1 (Soybean) I553L Mutant==
		+	<StructureSection load='3bnb' size='340' side='right' caption='[[3bnb]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bnb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BNB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f8n\|1f8n]], [[3bnc\|3bnc]], [[3bnd\|3bnd]], [[3bne\|3bne]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine max])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipoxygenase Lipoxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </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=3bnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bnb RCSB], [http://www.ebi.ac.uk/pdbsum/3bnb 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/bn/3bnb_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	This study examines the impact of a series of mutations at position 553 on the kinetic and structural properties of soybean lipoxygenase-1 (SLO-1). The previously uncharacterized mutants reported herein are I553L, I553V, and I553G. High-resolution x-ray studies of these mutants, together with the earlier studied I553A, show almost no structural change in relation to the WT-enzyme. By contrast, a progression in kinetic behavior occurs in which the decrease in the size of the side chain at position 553 leads to an increased importance of donor-acceptor distance sampling in the course of the hydrogen transfer process. These dynamical changes in behavior are interpreted in the context of two general classes of protein motions, preorganization and reorganization, with the latter including the distance sampling modes [Klinman JP (2006) Philos Trans R Soc London Ser B 361:1323-1331; Nagel Z, Klinman JP (2006) Chem Rev 106:3095-3118]. The aggregate data for SLO-1 show how judicious placement of hydrophobic side chains can influence enzyme catalysis via enhanced donor-acceptor hydrogenic wave function overlap.

-	~~{{STRUCTURE_3bnb\| PDB=3bnb \| SCENE= }}~~	+	Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1.,Meyer MP, Tomchick DR, Klinman JP Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1146-51. Epub 2008 Jan 23. PMID:18216254<ref>PMID:18216254</ref>

-	~~===Lipoxygenase-1 (Soybean) I553L Mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18216254}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3bnb]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Glycine_max Glycine max]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018216254<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Glycine max]]		[[Category: Glycine max]]
	[[Category: Lipoxygenase]]		[[Category: Lipoxygenase]]

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

2013-01-07T23:02:07Z

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

←Older revision

Revision as of 23:02, 7 January 2013

OCA at 23:02, 7 January 2013

2013-01-07T23:02:05Z

←Older revision		Revision as of 23:02, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3bnb.png\|left\|200px]]		[[Image:3bnb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bnb", 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_3bnb\| PDB=3bnb \| SCENE= }}		{{STRUCTURE_3bnb\| PDB=3bnb \| SCENE= }}

	===Lipoxygenase-1 (Soybean) I553L Mutant===		===Lipoxygenase-1 (Soybean) I553L Mutant===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18216254}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18216254 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18216254}}		{{ABSTRACT_PUBMED_18216254}}

	==About this Structure==		==About this Structure==
-	~~3BNB~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA].	+	[[3bnb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18216254~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018216254</ref><references group="xtra"/>
	[[Category: Glycine max]]		[[Category: Glycine max]]
	[[Category: Lipoxygenase]]		[[Category: Lipoxygenase]]
	[[Category: Tomchick, D R.]]		[[Category: Tomchick, D R.]]
-	[[Category: Cytoplasm]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]
Line 38:		Line 25:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Oxylipin biosynthesis]]		[[Category: Oxylipin biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:23:30 2009''

OCA at 12:23, 17 February 2009

2009-02-17T12:23:30Z

←Older revision		Revision as of 12:23, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BNB is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA].	+	3BNB is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNB OCA].

	==Reference==		==Reference==
-	Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1., Meyer MP, Tomchick DR, Klinman JP, Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1146-51. Epub 2008 Jan 23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18216254 18216254]~~	+	<ref group="xtra">PMID:18216254</ref><references group="xtra"/>
	[[Category: Glycine max]]		[[Category: Glycine max]]
	[[Category: Lipoxygenase]]		[[Category: Lipoxygenase]]
-	[[Category: Single protein]]
	[[Category: Tomchick, D R.]]		[[Category: Tomchick, D R.]]
	[[Category: Cytoplasm]]		[[Category: Cytoplasm]]
Line 40:		Line 39:
	[[Category: Oxylipin biosynthesis]]		[[Category: Oxylipin biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 19~~:47:~~33 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:23:30 2009''

OCA at 16:47, 28 July 2008

2008-07-28T16:47:35Z

←Older revision		Revision as of 16:47, 28 July 2008
Line 1:		Line 1:
-	[[Image:3bnb.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3bnb.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3bnb\| PDB=3bnb \| SCENE= }}		{{STRUCTURE_3bnb\| PDB=3bnb \| SCENE= }}

-	~~'''~~Lipoxygenase-1 (Soybean) I553L Mutant~~'''~~	+	===Lipoxygenase-1 (Soybean) I553L Mutant===


-	~~==Overview==~~	+	<!--
-	~~This study examines the impact of a series of mutations at position 553 on the kinetic and structural properties of soybean lipoxygenase~~-~~1 (SLO~~-~~1).~~ The ~~previously uncharacterized mutants reported herein are I553L~~, ~~I553V~~, ~~and I553G. High-resolution x-ray studies of these mutants, together with~~ the ~~earlier studied I553A, show almost no structural change in relation~~ to the ~~WT-enzyme. By contrast, a progression in kinetic behavior occurs in which the decrease in the size of the side chain~~ at ~~position 553 leads to an increased importance of donor-acceptor distance sampling in the course of the hydrogen transfer process~~. ~~These dynamical changes in behavior are interpreted in the context of two general classes of protein motions~~, ~~preorganization and reorganization, with~~ the ~~latter including the distance sampling modes [Klinman JP (2006) Philos Trans R Soc London Ser B 361:1323-1331; Nagel Z, Klinman JP (2006) Chem Rev 106:3095-3118]~~. ~~The aggregate data for SLO~~-~~1 show how judicious placement of hydrophobic side chains can influence enzyme catalysis via enhanced donor~~-~~acceptor hydrogenic wave function overlap.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18216254}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18216254 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18216254}}

	==About this Structure==		==About this Structure==
Line 35:		Line 39:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Oxylipin biosynthesis]]		[[Category: Oxylipin biosynthesis]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 20:55~~:47 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 19:47:33 2008''