2d1r - Revision history

OCA at 08:22, 25 October 2023

OCA — Wed, 25 Oct 2023 08:22:39 GMT

←Older revision		Revision as of 08:22, 25 October 2023
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	<StructureSection load='2d1r' size='340' side='right'caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d1r' size='340' side='right'caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Genji_firefly Genji firefly~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1R FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2~~-~~(6-HYDROXY-1~~,~~3-BENZOTHIAZOL-2-YL)-~~1~~,3-THIAZOL-4(5H)-ONE'>OLU</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]] 1.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CSO~~:~~S-HYDROXYCYSTEINE~~'>~~CSO~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</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;~~'>~~[[2d1s\|2d1s]], [[2d1t\|2d1t]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Photinus-luciferin_4~~-~~monooxygenase_~~(~~ATP~~-~~hydrolyzing) Photinus~~-~~luciferin 4~~-~~monooxygenase (ATP~~-~~hydrolyzing~~)], ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7]~~ </~~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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [https://pdbe.org/2d1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [https://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1r ProSAT], [https://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [https://pdbe.org/2d1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [https://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1r ProSAT], [https://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LUCI_LUCCR LUCI_LUCCR]] Produces green light with a wavelength of 544 nm.	+	[https://www.uniprot.org/uniprot/LUCI_LUCCR LUCI_LUCCR] Produces green light with a wavelength of 544 nm.
	== 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: Genji firefly]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hiratake, J]]	+	[[Category: Luciola cruciata]]
-	[[Category: Ichiyama, S]]	+	[[Category: Hiratake J]]
-	[[Category: Kato, H]]	+	[[Category: Ichiyama S]]
-	[[Category: Kobashi, N]]	+	[[Category: Kato H]]
-	[[Category: Nakatsu, T]]	+	[[Category: Kobashi N]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Nakatsu T]]
-	[[Category: Sakata, K]]	+	[[Category: Sakata K]]
-	[[Category: Saldanha, A]]	+	[[Category: Saldanha A]]
-	~~[[Category: Alpha+beta]]~~	+
-	~~[[Category: Alpha/beta]]~~	+
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 06:47, 10 November 2021

OCA — Wed, 10 Nov 2021 06:47:59 GMT

←Older revision		Revision as of 06:47, 10 November 2021
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	<StructureSection load='2d1r' size='340' side='right'caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d1r' size='340' side='right'caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Genji_firefly Genji firefly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D1R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Genji_firefly Genji firefly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d1s\|2d1s]], [[2d1t\|2d1t]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [~~http~~://pdbe.org/2d1r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1r ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [https://pdbe.org/2d1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [https://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1r ProSAT], [https://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LUCI_LUCCR LUCI_LUCCR]] Produces green light with a wavelength of 544 nm.	+	[[https://www.uniprot.org/uniprot/LUCI_LUCCR LUCI_LUCCR]] Produces green light with a wavelength of 544 nm.
	== 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==
	*[[Luciferase 3D structures\|Luciferase 3D structures]]		*[[Luciferase 3D structures\|Luciferase 3D structures]]
-	*[[Luciola cruciata luciferase\|Luciola cruciata luciferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:45, 4 March 2020

OCA — Wed, 04 Mar 2020 07:45:41 GMT

←Older revision		Revision as of 07:45, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP==		==Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP==
-	<StructureSection load='2d1r' size='340' side='right' caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2d1r' size='340' side='right'caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Genji_firefly Genji firefly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Genji_firefly Genji firefly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Luciferase\|Luciferase]]	+	*[[Luciferase 3D structures\|Luciferase 3D structures]]
	*[[Luciola cruciata luciferase\|Luciola cruciata luciferase]]		*[[Luciola cruciata luciferase\|Luciola cruciata luciferase]]
	== References ==		== References ==
Line 40:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Genji firefly]]		[[Category: Genji firefly]]
		+	[[Category: Large Structures]]
	[[Category: Hiratake, J]]		[[Category: Hiratake, J]]
	[[Category: Ichiyama, S]]		[[Category: Ichiyama, S]]

OCA at 06:31, 30 May 2018

OCA — Wed, 30 May 2018 06:31:39 GMT

←Older revision		Revision as of 06:31, 30 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP==		==Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP==
	<StructureSection load='2d1r' size='340' side='right' caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d1r' size='340' side='right' caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://pdbe.org/2d1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://pdbe.org/2d1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1r ProSAT], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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/d1/2d1r_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1r_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 06:09, 8 February 2016

OCA — Mon, 08 Feb 2016 06:09:17 GMT

←Older revision		Revision as of 06:09, 8 February 2016
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=2d1r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:39, 10 September 2015

OCA — Thu, 10 Sep 2015 08:39:18 GMT

←Older revision		Revision as of 08:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2d1r' size='340' side='right' caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d1r' size='340' side='right' caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Luciola_cruciata Luciola cruciata~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Genji_firefly Genji firefly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://pdbe.org/2d1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 2d1r" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Luciola cruciata~~]]	+	[[Category: Genji firefly]]
	[[Category: Hiratake, J]]		[[Category: Hiratake, J]]
	[[Category: Ichiyama, S]]		[[Category: Ichiyama, S]]

OCA at 21:12, 24 December 2014

OCA — Wed, 24 Dec 2014 21:12:15 GMT

←Older revision		Revision as of 21:12, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LUCI_LUCCR LUCI_LUCCR]] Produces green light with a wavelength of 544 nm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Luciola cruciata]]		[[Category: Luciola cruciata]]
-	[[Category: Hiratake, J.]]	+	[[Category: Hiratake, J]]
-	[[Category: Ichiyama, S.]]	+	[[Category: Ichiyama, S]]
-	[[Category: Kato, H.]]	+	[[Category: Kato, H]]
-	[[Category: Kobashi, N.]]	+	[[Category: Kobashi, N]]
-	[[Category: Nakatsu, T.]]	+	[[Category: Nakatsu, T]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sakata, K.]]	+	[[Category: Sakata, K]]
-	[[Category: Saldanha, A.]]	+	[[Category: Saldanha, A]]
	[[Category: Alpha+beta]]		[[Category: Alpha+beta]]
	[[Category: Alpha/beta]]		[[Category: Alpha/beta]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 01:54, 30 September 2014

OCA — Tue, 30 Sep 2014 01:54:01 GMT

←Older revision		Revision as of 01:54, 30 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2d1r\| PDB=2d1r \| SCENE= }}~~	+	==Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP==
-	===Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP===	+	<StructureSection load='2d1r' size='340' side='right' caption='[[2d1r]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_16541080}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1R FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=OLU:2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)-ONE'>OLU</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d1s\|2d1s]], [[2d1t\|2d1t]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=2d1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1r RCSB], [http://www.ebi.ac.uk/pdbsum/2d1r PDBsum], [http://www.topsan.org/Proteins/RSGI/2d1r TOPSAN]</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/d1/2d1r_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 ==
		+	Fireflies communicate with each other by emitting yellow-green to yellow-orange brilliant light. The bioluminescence reaction, which uses luciferin, Mg-ATP and molecular oxygen to yield an electronically excited oxyluciferin species, is carried out by the enzyme luciferase. Visible light is emitted during relaxation of excited oxyluciferin to its ground state. The high quantum yield of the luciferin/luciferase reaction and the change in bioluminescence colour caused by subtle structural differences in luciferase have attracted much research interest. In fact, a single amino acid substitution in luciferase changes the emission colour from yellow-green to red. Although the crystal structure of luciferase from the North American firefly (Photinus pyralis) has been described, the detailed mechanism for the bioluminescence colour change is still unclear. Here we report the crystal structures of wild-type and red mutant (S286N) luciferases from the Japanese Genji-botaru (Luciola cruciata) in complex with a high-energy intermediate analogue, 5'-O-[N-(dehydroluciferyl)-sulfamoyl]adenosine (DLSA). Comparing these structures to those of the wild-type luciferase complexed with AMP plus oxyluciferin (products) reveals a significant conformational change in the wild-type enzyme but not in the red mutant. This conformational change involves movement of the hydrophobic side chain of Ile 288 towards the benzothiazole ring of DLSA. Our results indicate that the degree of molecular rigidity of the excited state of oxyluciferin, which is controlled by a transient movement of Ile 288, determines the colour of bioluminescence during the emission reaction.

-	~~==About this Structure==~~	+	Structural basis for the spectral difference in luciferase bioluminescence.,Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H Nature. 2006 Mar 16;440(7082):372-6. PMID:16541080<ref>PMID:16541080</ref>
-	~~[[2d1r]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Luciola_cruciata Luciola cruciata]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=2D1R OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Luciferase\|Luciferase]]		*[[Luciferase\|Luciferase]]
	*[[Luciola cruciata luciferase\|Luciola cruciata luciferase]]		*[[Luciola cruciata luciferase\|Luciola cruciata luciferase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016541080<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Luciola cruciata]]		[[Category: Luciola cruciata]]
	[[Category: Hiratake, J.]]		[[Category: Hiratake, J.]]

OCA at 10:27, 11 March 2013

OCA — Mon, 11 Mar 2013 10:27:27 GMT

←Older revision		Revision as of 10:27, 11 March 2013
Line 1:		Line 1:
-	[[Image:2d1r.png\|left\|200px]]
-
	{{STRUCTURE_2d1r\| PDB=2d1r \| SCENE= }}		{{STRUCTURE_2d1r\| PDB=2d1r \| SCENE= }}
-
	===Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP===		===Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP===
-
	{{ABSTRACT_PUBMED_16541080}}		{{ABSTRACT_PUBMED_16541080}}

OCA at 09:11, 20 October 2012

OCA — Sat, 20 Oct 2012 09:11:39 GMT

←Older revision		Revision as of 09:11, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2d1r]] is a 1 chain structure ~~of [[Luciferase]]~~ with sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA].	+	[[2d1r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA].

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