2g5z - Revision history

OCA at 09:35, 30 August 2023

OCA — Wed, 30 Aug 2023 09:35:58 GMT

←Older revision		Revision as of 09:35, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2g5z' size='340' side='right'caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2g5z' size='340' side='right'caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G5Z 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]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=~~NME~~:~~METHYLAMINE~~'>~~NME~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</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;~~'>~~[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]~~</~~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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [https://pdbe.org/2g5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [https://www.ebi.ac.uk/pdbsum/2g5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g5z 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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [https://pdbe.org/2g5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [https://www.ebi.ac.uk/pdbsum/2g5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g5z 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]]
Line 38:		Line 36:
	__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: Kassmann~~, C J~~]]	+	[[Category: Kassmann CJ]]
-	[[Category: Tainer~~, J A]]~~	+	[[Category: Tainer JA]]
-	~~[[Category: Biosynthesis]]~~	+
-	~~[[Category: Chromophore]]~~	+
-	~~[[Category: Decarboxylation]]~~	+
-	~~[[Category: Luminescent protein]]~~	+
-	~~[[Category: Peptide hydrolysis]]~~	+
-	~~[[Category: Post-translational modification~~]]	+

OCA at 18:47, 10 March 2021

OCA — Wed, 10 Mar 2021 18:47:53 GMT

←Older revision		Revision as of 18:47, 10 March 2021
Line 1:		Line 1:

	==Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation==		==Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation==
-	<StructureSection load='2g5z' size='340' side='right' caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2g5z' size='340' side='right'caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2G5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G5Z 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=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [~~http~~://pdbe.org/2g5z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2g5z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2g5z 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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [https://pdbe.org/2g5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [https://www.ebi.ac.uk/pdbsum/2g5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g5z 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]]
Line 33:		Line 33:

	==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 06:40, 20 June 2018

OCA — Wed, 20 Jun 2018 06:40:29 GMT

←Older revision		Revision as of 06:40, 20 June 2018
Line 1:		Line 1:
		+
	==Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation==		==Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation==
	<StructureSection load='2g5z' size='340' side='right' caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2g5z' size='340' side='right' caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://pdbe.org/2g5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z 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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://pdbe.org/2g5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2g5z 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/g5/2g5z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/2g5z_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 10:33, 9 February 2016

OCA — Tue, 09 Feb 2016 10:33:38 GMT

←Older revision		Revision as of 10:33, 9 February 2016
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	<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=2g5z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:25, 10 September 2015

OCA — Thu, 10 Sep 2015 21:25:18 GMT

←Older revision		Revision as of 21:25, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2g5z' size='340' side='right' caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2g5z' size='340' side='right' caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G5Z 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=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z 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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://pdbe.org/2g5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z PDBsum]</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 2g5z" 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 06:17, 25 December 2014

OCA — Thu, 25 Dec 2014 06:17:43 GMT

←Older revision		Revision as of 06:17, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G5Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G5Z 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=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z 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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z 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: Kassmann, C J.]]	+	[[Category: Kassmann, C J]]
-	[[Category: Tainer, J A.]]	+	[[Category: Tainer, J A]]
	[[Category: Biosynthesis]]		[[Category: Biosynthesis]]
	[[Category: Chromophore]]		[[Category: Chromophore]]

OCA at 05:11, 3 October 2014

OCA — Fri, 03 Oct 2014 05:11:31 GMT

←Older revision		Revision as of 05:11, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2g5z.~~png~~\|~~left~~\|200px]]	+	==Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation==
		+	<StructureSection load='2g5z' size='340' side='right' caption='[[2g5z]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2g5z]] is a 2 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=2G5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G5Z 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=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g16\|2g16]], [[2g2s\|2g2s]], [[2g3d\|2g3d]]</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=2g5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g5z RCSB], [http://www.ebi.ac.uk/pdbsum/2g5z 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/g5/2g5z_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The green fluorescent protein (GFP) creates a fluorophore out of three sequential amino acids by promoting spontaneous posttranslational modifications. Here, we use high-resolution crystallography to characterize GFP variants that not only undergo peptide backbone cyclization but additional denaturation-induced peptide backbone fragmentation, native peptide hydrolysis, and decarboxylation reactions. Our analyses indicate that architectural features that favor GFP peptide cyclization also drive peptide hydrolysis. These results are relevant for the maturation pathways of GFP homologues, such as the kindling fluorescent protein and the Kaede protein, which use backbone cleavage to red-shift the spectral properties of their chromophores. We further propose a photochemical mechanism for the decarboxylation reaction, supporting a role for the GFP protein environment in facilitating radical formation and one-electron chemistry, which may be important in activating oxygen for the oxidation step of chromophore biosynthesis. Together, our results characterize GFP posttranslational modification chemistry with implications for the energetic landscape of backbone cyclization and subsequent reactions, and for the rational design of predetermined spontaneous backbone cyclization and cleavage reactions.

-	~~{{STRUCTURE_2g5z\| PDB=2g5z \| SCENE= }}~~	+	Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation.,Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED J Am Chem Soc. 2006 Apr 12;128(14):4685-93. PMID:16594705<ref>PMID:16594705</ref>

-	~~===Structure~~ of ~~S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16594705}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2g5z]] is a 2 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=2G5Z 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:016594705<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aequorea victoria]]		[[Category: Aequorea victoria]]
	[[Category: Barondeau, D P.]]		[[Category: Barondeau, D P.]]

OCA at 13:35, 20 October 2012

OCA — Sat, 20 Oct 2012 13:35:27 GMT

←Older revision		Revision as of 13:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2g5z]] is a 2 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=2G5Z OCA].	+	[[2g5z]] is a 2 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=2G5Z OCA].

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

OCA: Protected "2g5z" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 12:27:58 GMT

Protected "2g5z" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:27, 26 July 2012

OCA at 12:27, 26 July 2012

OCA — Thu, 26 Jul 2012 12:27:57 GMT

←Older revision		Revision as of 12:27, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2g5z.png\|left\|200px]]		[[Image:2g5z.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2g5z", 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_2g5z\| PDB=2g5z \| SCENE= }}		{{STRUCTURE_2g5z\| PDB=2g5z \| SCENE= }}

	===Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation===		===Structure of S65G Y66S GFP variant after spontaneous peptide hydrolysis and decarboxylation===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16594705}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16594705 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16594705}}		{{ABSTRACT_PUBMED_16594705}}

	==About this Structure==		==About this Structure==
-	~~2G5Z~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=2G5Z OCA].	+	[[2g5z]] is a 2 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=2G5Z OCA].
		+
		+	==See Also==
		+	*[[Alyssa Marsico/Sandbox 1\|Alyssa Marsico/Sandbox 1]]
		+	*[[Devon McCarthy/Sandbox 1\|Devon McCarthy/Sandbox 1]]
		+	*[[Green Fluorescent Protein\|Green Fluorescent Protein]]
		+	*[[Sandbox104\|Sandbox104]]
		+	*[[User:Joanne Lau/Sandbox 5\|User:Joanne Lau/Sandbox 5]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16594705~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016594705</ref><references group="xtra"/>
	[[Category: Aequorea victoria]]		[[Category: Aequorea victoria]]
	[[Category: Barondeau, D P.]]		[[Category: Barondeau, D P.]]
Line 32:		Line 27:
	[[Category: Chromophore]]		[[Category: Chromophore]]
	[[Category: Decarboxylation]]		[[Category: Decarboxylation]]
		+	[[Category: Luminescent protein]]
	[[Category: Peptide hydrolysis]]		[[Category: Peptide hydrolysis]]
	[[Category: Post-translational modification]]		[[Category: Post-translational modification]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:10:29 2009''