2z6y - Revision history

OCA at 13:23, 1 November 2023

OCA — Wed, 01 Nov 2023 13:23:46 GMT

←Older revision		Revision as of 13:23, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2z6y' size='340' side='right'caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2z6y' size='340' side='right'caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Echinophyllia_sp.~~_sc22~~ Echinophyllia sp. ~~sc22~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Echinophyllia_sp._SC22 Echinophyllia sp. SC22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</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]] 2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [https://pdbe.org/2z6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [https://www.ebi.ac.uk/pdbsum/2z6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6y 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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [https://pdbe.org/2z6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [https://www.ebi.ac.uk/pdbsum/2z6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6y ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5TLG6_9CNID Q5TLG6_9CNID]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Echinophyllia sp. ~~sc22~~]]	+	[[Category: Echinophyllia sp. SC22]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jeyakanthan, J]]	+	[[Category: Jeyakanthan J]]
-	[[Category: Kikuchi, A]]	+	[[Category: Kikuchi A]]
-	[[Category: Miyawaki, A]]	+	[[Category: Miyawaki A]]
-	[[Category: Mizuno, H]]	+	[[Category: Mizuno H]]
-	[[Category: Shiro, Y]]	+	[[Category: Shiro Y]]
-	[[Category: Taka, J]]	+	[[Category: Taka J]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Gfp-like protein]]~~	+
-	~~[[Category: Photochromism~~]]	+

OCA at 10:47, 8 December 2021

OCA — Wed, 08 Dec 2021 10:47:16 GMT

←Older revision		Revision as of 10:47, 8 December 2021
Line 1:		Line 1:

	==Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state==		==Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state==
-	<StructureSection load='2z6y' size='340' side='right' caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2z6y' size='340' side='right'caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</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=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [~~http~~://pdbe.org/2z6y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z6y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6y 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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [https://pdbe.org/2z6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [https://www.ebi.ac.uk/pdbsum/2z6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6y ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Echinophyllia sp. sc22]]		[[Category: Echinophyllia sp. sc22]]
		+	[[Category: Large Structures]]
	[[Category: Jeyakanthan, J]]		[[Category: Jeyakanthan, J]]
	[[Category: Kikuchi, A]]		[[Category: Kikuchi, A]]

OCA at 09:27, 17 October 2018

OCA — Wed, 17 Oct 2018 09:27:37 GMT

←Older revision		Revision as of 09:27, 17 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state==		==Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state==
	<StructureSection load='2z6y' size='340' side='right' caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2z6y' size='340' side='right' caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://pdbe.org/2z6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y 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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://pdbe.org/2z6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6y ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z6y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z6y_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 00:24, 10 February 2016

OCA — Wed, 10 Feb 2016 00:24:08 GMT

←Older revision		Revision as of 00:24, 10 February 2016
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y 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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://pdbe.org/2z6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=2z6y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 2z6y" style="background-color:#fffaf0;"></div>

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

OCA at 10:46, 20 January 2015

OCA — Tue, 20 Jan 2015 10:46:27 GMT

←Older revision		Revision as of 10:46, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</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=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y 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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Echinophyllia sp. sc22]]		[[Category: Echinophyllia sp. sc22]]
-	[[Category: Jeyakanthan, J.]]	+	[[Category: Jeyakanthan, J]]
-	[[Category: Kikuchi, A.]]	+	[[Category: Kikuchi, A]]
-	[[Category: Miyawaki, A.]]	+	[[Category: Miyawaki, A]]
-	[[Category: Mizuno, H.]]	+	[[Category: Mizuno, H]]
-	[[Category: Shiro, Y.]]	+	[[Category: Shiro, Y]]
-	[[Category: Taka, J.]]	+	[[Category: Taka, J]]
	[[Category: Fluorescent protein]]		[[Category: Fluorescent protein]]
	[[Category: Gfp-like protein]]		[[Category: Gfp-like protein]]
	[[Category: Photochromism]]		[[Category: Photochromism]]

OCA at 09:14, 29 September 2014

OCA — Mon, 29 Sep 2014 09:14:06 GMT

←Older revision		Revision as of 09:14, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2z6y.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state==
		+	<StructureSection load='2z6y' size='340' side='right' caption='[[2z6y]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z6y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z6Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z6x\|2z6x]], [[2z6z\|2z6z]], [[2z1o\|2z1o]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</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=2z6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z6y RCSB], [http://www.ebi.ac.uk/pdbsum/2z6y 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/z6/2z6y_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 structural basis for the photochromism in the fluorescent protein Dronpa is poorly understood, because the crystal structures of the bright state of the protein did not provide an answer to the mechanism of the photochromism, and structural determination of the dark state has been elusive. We performed NMR analyses of Dronpa in solution at ambient temperatures to find structural flexibility of the protein in the dark state. Light-induced changes in interactions between the chromophore and beta-barrel are responsible for switching between the two states. In the bright state, the apex of the chromophore tethers to the barrel by a hydrogen bond, and an imidazole ring protruding from the barrel stabilizes the plane of the chromophore. These interactions are disrupted by strong illumination with blue light, and the chromophore, together with a part of the beta-barrel, becomes flexible, leading to a nonradiative decay process.

-	~~{{STRUCTURE_2z6y\| PDB=2z6y \| SCENE= }}~~	+	Light-dependent regulation of structural flexibility in a photochromic fluorescent protein.,Mizuno H, Mal TK, Walchli M, Kikuchi A, Fukano T, Ando R, Jeyakanthan J, Taka J, Shiro Y, Ikura M, Miyawaki A Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9227-32. Epub 2008 Jun 23. PMID:18574155<ref>PMID:18574155</ref>

-	~~===Crystal structure~~ of ~~a photoswitchable GFP-like protein Dronpa in~~ the ~~bright-state===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18574155}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2z6y]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Echinophyllia_sp~~.~~_sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].~~	+

	==See Also==		==See Also==
	*[[Dronpa\|Dronpa]]		*[[Dronpa\|Dronpa]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018574155<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Echinophyllia sp. sc22]]		[[Category: Echinophyllia sp. sc22]]
	[[Category: Jeyakanthan, J.]]		[[Category: Jeyakanthan, J.]]

OCA at 15:39, 20 October 2012

OCA — Sat, 20 Oct 2012 15:39:46 GMT

←Older revision		Revision as of 15:39, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2z6y]] is a 4 chain structure ~~of [[Dronpa]]~~ with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].	+	[[2z6y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].

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

OCA: Protected "2z6y" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 19:05:15 GMT

Protected "2z6y" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:05, 26 July 2012

OCA at 19:05, 26 July 2012

OCA — Thu, 26 Jul 2012 19:05:13 GMT

←Older revision		Revision as of 19:05, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z6y.png\|left\|200px]]		[[Image:2z6y.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z6y", 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_2z6y\| PDB=2z6y \| SCENE= }}		{{STRUCTURE_2z6y\| PDB=2z6y \| SCENE= }}

	===Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state===		===Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18574155}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18574155 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18574155}}		{{ABSTRACT_PUBMED_18574155}}

	==About this Structure==		==About this Structure==
-	~~2Z6Y~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].	+	[[2z6y]] is a 4 chain structure of [[Dronpa]] with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].
		+
		+	==See Also==
		+	*[[Dronpa\|Dronpa]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18574155~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018574155</ref><references group="xtra"/>
	[[Category: Echinophyllia sp. sc22]]		[[Category: Echinophyllia sp. sc22]]
	[[Category: Jeyakanthan, J.]]		[[Category: Jeyakanthan, J.]]
Line 34:		Line 25:
	[[Category: Gfp-like protein]]		[[Category: Gfp-like protein]]
	[[Category: Photochromism]]		[[Category: Photochromism]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:56:05 2009''

OCA at 11:56, 17 February 2009

OCA — Tue, 17 Feb 2009 11:56:07 GMT

←Older revision		Revision as of 11:56, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z6Y is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].	+	2Z6Y is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Y OCA].

	==Reference==		==Reference==
-	Light-dependent regulation of structural flexibility in a photochromic fluorescent protein., Mizuno H, Mal TK, Walchli M, Kikuchi A, Fukano T, Ando R, Jeyakanthan J, Taka J, Shiro Y, Ikura M, Miyawaki A, Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9227-32. Epub 2008 Jun 23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18574155 18574155]~~	+	<ref group="xtra">PMID:18574155</ref><references group="xtra"/>
	[[Category: Echinophyllia sp. sc22]]		[[Category: Echinophyllia sp. sc22]]
-	[[Category: Single protein]]
	[[Category: Jeyakanthan, J.]]		[[Category: Jeyakanthan, J.]]
	[[Category: Kikuchi, A.]]		[[Category: Kikuchi, A.]]
Line 36:		Line 35:
	[[Category: Photochromism]]		[[Category: Photochromism]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 19:~~13:~~40 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:56:05 2009''