3dpw - Revision history

OCA at 12:50, 30 August 2023

2023-08-30T12:50:57Z

←Older revision		Revision as of 12:50, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3dpw' size='340' side='right'caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='3dpw' size='340' side='right'caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPW FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4~~-[~~(4-HYDROXYPHENYL)METHYLIDENE~~]~~-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-~~1~~-YL}ACETIC+ACID'>CR2</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]] 1.59Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;'>~~[~~[1huy\|1huy]~~], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [https://pdbe.org/3dpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [https://www.ebi.ac.uk/pdbsum/3dpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpw 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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [https://pdbe.org/3dpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [https://www.ebi.ac.uk/pdbsum/3dpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpw 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: Barstow, B]]	+	[[Category: Barstow B]]
-	[[Category: Kim~~, C U]]~~	+	[[Category: Kim CU]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Chromophore]]~~	+
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: High pressure]]~~	+
-	~~[[Category: Luminescence]]~~	+
-	~~[[Category: Luminescent protein]]~~	+
-	~~[[Category: Photoprotein]]~~	+
-	~~[[Category: Yellow fluorescent protein~~]]	+

OCA at 19:26, 20 October 2021

2021-10-20T19:26:32Z

←Older revision		Revision as of 19:26, 20 October 2021
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	==Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures==		==Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures==
-	<StructureSection load='3dpw' size='340' side='right' caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='3dpw' size='340' side='right'caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPW FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [~~http~~://pdbe.org/3dpw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dpw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpw 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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [https://pdbe.org/3dpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [https://www.ebi.ac.uk/pdbsum/3dpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpw 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 32:		Line 32:

	==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 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Aeqvi]]		[[Category: Aeqvi]]
		+	[[Category: Large Structures]]
	[[Category: Barstow, B]]		[[Category: Barstow, B]]
	[[Category: Kim, C U]]		[[Category: Kim, C U]]

OCA at 09:15, 14 November 2018

2018-11-14T09:15:58Z

←Older revision		Revision as of 09:15, 14 November 2018
Line 1:		Line 1:
		+
	==Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures==		==Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures==
	<StructureSection load='3dpw' size='340' side='right' caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='3dpw' size='340' side='right' caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://pdbe.org/3dpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw 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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://pdbe.org/3dpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpw_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 04:06, 10 February 2016

2016-02-10T04:06:57Z

←Older revision		Revision as of 04:06, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3dpw' size='340' side='right' caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='3dpw' size='340' side='right' caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPW FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw 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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://pdbe.org/3dpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3dpw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3dpw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aequorea victoria~~]]	+	[[Category: Aeqvi]]
	[[Category: Barstow, B]]		[[Category: Barstow, B]]
	[[Category: Kim, C U]]		[[Category: Kim, C U]]

OCA at 11:41, 25 December 2014

2014-12-25T11:41:08Z

←Older revision		Revision as of 11:41, 25 December 2014
Line 8:		Line 8:
	<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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw 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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw 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]]

OCA at 17:47, 21 December 2014

2014-12-21T17:47:34Z

←Older revision		Revision as of 17:47, 21 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3dpw.~~png~~\|~~left~~\|200px]]	+	==Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures==
		+	<StructureSection load='3dpw' size='340' side='right' caption='[[3dpw]], [[Resolution\|resolution]] 1.59Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dpw]] 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=3DPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPW FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1huy\|1huy]], [[1yfp\|1yfp]], [[2yfp\|2yfp]], [[1f0b\|1f0b]], [[1f09\|1f09]], [[3dpx\|3dpx]], [[3dpz\|3dpz]], [[3dq1\|3dq1]], [[3dq2\|3dq2]], [[3dq3\|3dq3]], [[3dq4\|3dq4]], [[3dq5\|3dq5]], [[3dq6\|3dq6]], [[3dq7\|3dq7]], [[3dq8\|3dq8]], [[3dq9\|3dq9]], [[3dqa\|3dqa]], [[3dqc\|3dqc]], [[3dqd\|3dqd]], [[3dqe\|3dqe]], [[3dqf\|3dqf]], [[3dqh\|3dqh]], [[3dqi\|3dqi]], [[3dqj\|3dqj]], [[3dqk\|3dqk]], [[3dql\|3dql]], [[3dqm\|3dqm]], [[3dqn\|3dqn]], [[3dqo\|3dqo]], [[3dqu\|3dqu]]</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='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=3dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpw RCSB], [http://www.ebi.ac.uk/pdbsum/3dpw 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/dp/3dpw_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 ==
		+	A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To elucidate this relationship, we have investigated a fluorescent protein, citrine, as a model system under high-pressure perturbation. The protein has been compressed to produce deformations of its chromophore by applying a high-pressure cryocooling technique. A closely spaced series of x-ray crystallographic structures reveals that the chromophore undergoes a progressive deformation of up to 0.8 A at an applied pressure of 500 MPa. It is experimentally demonstrated that the structural motion is directly correlated with the progressive fluorescence shift of citrine from yellow to green under these conditions. This protein is therefore highly sensitive to subangstrom deformations and its function must be understood at the subangstrom level. These results have significant implications for protein function prediction and biomolecule design and engineering, because they suggest methods to tune protein function by modification of the protein scaffold.

-	~~{{STRUCTURE_3dpw\| PDB=3dpw \| SCENE= }}~~	+	Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.,Barstow B, Ando N, Kim CU, Gruner SM Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13362-6. Epub 2008 Sep 3. PMID:18768811<ref>PMID:18768811</ref>

-	~~===Structure~~ of the ~~Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18768811}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3dpw]] 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=3DPW 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:018768811<~~/~~ref~~><~~ref group="xtra">PMID:015983410</ref><references group="xtra"~~/>	+
	[[Category: Aequorea victoria]]		[[Category: Aequorea victoria]]
-	[[Category: Barstow, B.]]	+	[[Category: Barstow, B]]
-	[[Category: Kim, C U.]]	+	[[Category: Kim, C U]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Chromophore]]		[[Category: Chromophore]]

OCA at 16:16, 20 October 2012

2012-10-20T16:16:49Z

←Older revision		Revision as of 16:16, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3dpw]] 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=3DPW OCA].	+	[[3dpw]] 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=3DPW OCA].

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

OCA at 21:09, 26 July 2012

2012-07-26T21:09:43Z

←Older revision		Revision as of 21:09, 26 July 2012
Line 1:		Line 1:
	[[Image:3dpw.png\|left\|200px]]		[[Image:3dpw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dpw", 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_3dpw\| PDB=3dpw \| SCENE= }}		{{STRUCTURE_3dpw\| PDB=3dpw \| SCENE= }}

	===Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures===		===Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 1: Structure 1 in a Series of 26 High Pressure Structures===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18768811}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18768811 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18768811}}		{{ABSTRACT_PUBMED_18768811}}

	==About this Structure==		==About this Structure==
-	[[3dpw]] is a 1 chain structure of [[Green Fluorescent Protein]] 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=3DPW OCA].	+	[[3dpw]] 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=3DPW OCA].

	==See Also==		==See Also==
-	*[[Green Fluorescent Protein]]	+	*[[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:~~18768811~~</ref><ref group="xtra">PMID:~~15983410~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018768811</ref><ref group="xtra">PMID:015983410</ref><references group="xtra"/>
	[[Category: Aequorea victoria]]		[[Category: Aequorea victoria]]
	[[Category: Barstow, B.]]		[[Category: Barstow, B.]]

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

2011-03-14T19:38:53Z

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

←Older revision

Revision as of 19:38, 14 March 2011

OCA at 19:38, 14 March 2011

2011-03-14T19:38:52Z

←Older revision		Revision as of 19:38, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3dpw.png\|left\|200px]]		[[Image:3dpw.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~3DPW~~ is a 1 chain structure of 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=3DPW OCA].	+	[[3dpw]] is a 1 chain structure of [[Green Fluorescent Protein]] 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=3DPW OCA].
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein]]

	==Reference==		==Reference==
Line 35:		Line 37:
	[[Category: Photoprotein]]		[[Category: Photoprotein]]
	[[Category: Yellow fluorescent protein]]		[[Category: Yellow fluorescent protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:18:04 2009''