2awk - Revision history

OCA at 00:47, 21 November 2024

2024-11-21T00:47:31Z

← Older revision		Revision as of 00:47, 21 November 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aw/2awk_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aw/2awk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 07:30, 23 August 2023

2023-08-23T07:30:51Z

← Older revision		Revision as of 07:30, 23 August 2023
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	<StructureSection load='2awk' size='340' side='right'caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='2awk' size='340' side='right'caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aeqvi Aeqvi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AWK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AWK FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.15Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;~~'>~~[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]~~</~~div~~>~~</td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])~~</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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [https://pdbe.org/2awk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [https://www.ebi.ac.uk/pdbsum/2awk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2awk 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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [https://pdbe.org/2awk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [https://www.ebi.ac.uk/pdbsum/2awk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2awk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.		[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	== 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: ~~Aeqvi~~]]		[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Barondeau~~, D P~~]]		[[Category: Barondeau DP]]
	[[Category: Getzoff~~, E D~~]]		[[Category: Getzoff ED]]
	[[Category: Hitomi, C]]		[[Category: Hitomi C]]
	[[Category: Kassmann~~, C J~~]]		[[Category: Kassmann CJ]]
	[[Category: Tainer~~, J A~~]]		[[Category: Tainer JA]]
	[[Category: Wood~~, T I]]~~		[[Category: Wood TI]]
	~~[[Category: Gfp chromophore formation barrel]]~~
	~~[[Category: Luminescent protein]]~~
	~~[[Category: Slow maturation mutant~~]]

OCA at 08:39, 27 January 2021

2021-01-27T08:39:13Z

← Older revision		Revision as of 08:39, 27 January 2021
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	==GFP R96M mature chromophore==		==GFP R96M mature chromophore==
	<StructureSection load='2awk' size='340' side='right' caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='2awk' size='340' side='right'caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2AWK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AWK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [~~http~~://pdbe.org/2awk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2awk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2awk 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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [https://pdbe.org/2awk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [https://www.ebi.ac.uk/pdbsum/2awk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2awk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.		[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	== 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==
	*[[Green Fluorescent Protein\|Green Fluorescent Protein]]		*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Aeqvi]]		[[Category: Aeqvi]]
			[[Category: Large Structures]]
	[[Category: Barondeau, D P]]		[[Category: Barondeau, D P]]
	[[Category: Getzoff, E D]]		[[Category: Getzoff, E D]]

OCA at 07:00, 9 May 2018

2018-05-09T07:00:16Z

← Older revision		Revision as of 07:00, 9 May 2018
Line 1:		Line 1:

	==GFP R96M mature chromophore==		==GFP R96M mature chromophore==
	<StructureSection load='2awk' size='340' side='right' caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='2awk' size='340' side='right' caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://pdbe.org/2awk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk 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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://pdbe.org/2awk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2awk 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/aw/2awk_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aw/2awk_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 02:32, 8 February 2016

2016-02-08T02:32:07Z

← Older revision		Revision as of 02:32, 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=2awk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:02, 10 September 2015

2015-09-10T07:02:03Z

← Older revision		Revision as of 07:02, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2awk' size='340' side='right' caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='2awk' size='340' side='right' caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aequorea_victoria Aequorea victoria~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AWK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AWK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 ~~Aequorea victoria~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 AEQVI])</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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk 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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://pdbe.org/2awk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2awk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aequorea victoria~~]]		[[Category: Aeqvi]]
	[[Category: Barondeau, D P]]		[[Category: Barondeau, D P]]
	[[Category: Getzoff, E D]]		[[Category: Getzoff, E D]]

OCA at 19:55, 24 December 2014

2014-12-24T19:55:15Z

← Older revision		Revision as of 19:55, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AWK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AWK FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 Aequorea victoria])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 Aequorea victoria])</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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk 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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Aequorea victoria]]		[[Category: Aequorea victoria]]
	[[Category: Barondeau, D P.]]		[[Category: Barondeau, D P]]
	[[Category: Getzoff, E D.]]		[[Category: Getzoff, E D]]
	[[Category: Hitomi, C.]]		[[Category: Hitomi, C]]
	[[Category: Kassmann, C J.]]		[[Category: Kassmann, C J]]
	[[Category: Tainer, J A.]]		[[Category: Tainer, J A]]
	[[Category: Wood, T I.]]		[[Category: Wood, T I]]
	[[Category: Gfp chromophore formation barrel]]		[[Category: Gfp chromophore formation barrel]]
	[[Category: Luminescent protein]]		[[Category: Luminescent protein]]
	[[Category: Slow maturation mutant]]		[[Category: Slow maturation mutant]]

OCA at 05:23, 3 October 2014

2014-10-03T05:23:14Z

← Older revision		Revision as of 05:23, 3 October 2014
Line 1:		Line 1:
	[[Image:~~2awk~~.~~png~~\|~~left~~\|~~200px~~]]		==GFP R96M mature chromophore==
			<StructureSection load='2awk' size='340' side='right' caption='[[2awk]], [[Resolution\|resolution]] 1.15Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2awk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AWK FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2awj\|2awj]], [[2awl\|2awl]], [[2awm\|2awm]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 Aequorea victoria])</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=2awk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2awk RCSB], [http://www.ebi.ac.uk/pdbsum/2awk 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/aw/2awk_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 ==
			Aequoria victoria green fluorescent protein (GFP) is a revolutionary molecular biology tool because of its spontaneous peptide backbone cyclization and chromophore formation from residues Ser65, Tyr66, and Gly67. Here we use structure-based design, comprehensive targeted mutagenesis, and high-resolution crystallography to probe the significant functional role of conserved Arg96 (R96) in chromophore maturation. The R96M GFP variant, in which the R96M side chain is similar in volume but lacks the R96 positive charge, exhibits dramatically slower chromophore maturation kinetics (from hours to months). Comparison of the precyclized conformation of the chromophore-forming residues with the mature R96M chromophore reveals a similar Y66 conformer, contrary to the large Y66 conformational change previously defined in the slowly maturing R96A variant [Barondeau, D. P., Putnam, C. D., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 12111-12116]. Comprehensive R96 mutagenesis and fluorescent colony screening indicate that only the R96K substitution restores wild-type maturation kinetics. Further, we show that the slowly maturing R96A variant can be complemented with a Q183R second-site mutation designed to restore the missing R96 positive charge and rapid fluorophore biosynthesis. Moreover, comparative structural analysis of R96M, R96K, R96A/Q183R, and wild-type GFP reveals the importance of the presence of positive charge, rather than its exact position. Together, these structural, mutational, and biochemical results establish a pivotal role for the R96 positive charge in accelerating the GFP post-translational modification, with implications for peptide backbone cyclization in GFP, its homologues, and related biological systems.

	~~{{STRUCTURE_2awk\| PDB=2awk \| SCENE= }}~~		Defining the role of arginine 96 in green fluorescent protein fluorophore biosynthesis.,Wood TI, Barondeau DP, Hitomi C, Kassmann CJ, Tainer JA, Getzoff ED Biochemistry. 2005 Dec 13;44(49):16211-20. PMID:16331981<ref>PMID:16331981</ref>

	~~===GFP R96M mature chromophore===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16331981}}~~

	~~==About this Structure==~~
	~~[[2awk]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Aequorea_victoria Aequorea victoria]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2AWK OCA].~~

	==See Also==		==See Also==
	*[[Alyssa Marsico/Sandbox 1\|Alyssa Marsico/Sandbox 1]]
	*[[Devon McCarthy/Sandbox 1\|Devon McCarthy/Sandbox 1]]
	*[[Green Fluorescent Protein\|Green Fluorescent Protein]]		*[[Green Fluorescent Protein\|Green Fluorescent Protein]]
	*[[Sandbox104\|Sandbox104]]		== References ==
	*[[User:Joanne Lau/Sandbox 5\|User:Joanne Lau/Sandbox 5]]		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:016331981<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Aequorea victoria]]		[[Category: Aequorea victoria]]
	[[Category: Barondeau, D P.]]		[[Category: Barondeau, D P.]]

OCA at 08:36, 20 October 2012

2012-10-20T08:36:30Z

← Older revision		Revision as of 08:36, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2awk]] is a 1 chain structure ~~of [[Alyssa Marsico/Sandbox 1]], [[Devon McCarthy/Sandbox 1]], [[Green Fluorescent Protein]], [[Sandbox104]] and [[User:Joanne Lau/Sandbox 5]]~~ with sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA].		[[2awk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWK OCA].

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

OCA: Protected "2awk" [edit=sysop:move=sysop]

2012-07-25T20:08:34Z

Protected "2awk" [edit=sysop:move=sysop]

← Older revision	Revision as of 20:08, 25 July 2012
(No difference)