5exc - Revision history

OCA at 09:37, 15 November 2023

OCA — Wed, 15 Nov 2023 09:37:52 GMT

←Older revision		Revision as of 09:37, 15 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Dendronephthya_sp._SSAL-2002 Dendronephthya sp. SSAL-2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EXC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Dendronephthya_sp._SSAL-2002 Dendronephthya sp. SSAL-2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EXC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</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]] 2.14Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [https://pdbe.org/5exc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [https://www.ebi.ac.uk/pdbsum/5exc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc 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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [https://pdbe.org/5exc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [https://www.ebi.ac.uk/pdbsum/5exc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:39, 18 January 2023

OCA — Wed, 18 Jan 2023 07:39:26 GMT

←Older revision		Revision as of 07:39, 18 January 2023
Line 3:		Line 3:
	<StructureSection load='5exc' size='340' side='right'caption='[[5exc]], [[Resolution\|resolution]] 2.14Å' scene=''>		<StructureSection load='5exc' size='340' side='right'caption='[[5exc]], [[Resolution\|resolution]] 2.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Dendronephthya_sp.~~_ssal~~-2002 Dendronephthya sp. ~~ssal~~-2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EXC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Dendronephthya_sp._SSAL-2002 Dendronephthya sp. SSAL-2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EXC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [https://pdbe.org/5exc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [https://www.ebi.ac.uk/pdbsum/5exc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [~~http~~://pdbe.org/5exc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5exc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8T6U0_9CNID Q8T6U0_9CNID]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dendronephthya sp. ~~ssal~~-2002]]	+	[[Category: Dendronephthya sp. SSAL-2002]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pletnev~~, S V~~]]	+	[[Category: Pletnev SV]]
-	[[Category: Pletnev~~, V Z~~]]	+	[[Category: Pletnev VZ]]
-	[[Category: Pletneva~~, N V]]~~	+	[[Category: Pletneva NV]]
-	~~[[Category: Beta-barrel]]~~	+
-	~~[[Category: Biomarker]]~~	+
-	~~[[Category: Chromophore]]~~	+
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Photoswitchable fluorescent protein~~]]	+

OCA at 07:49, 29 April 2020

OCA — Wed, 29 Apr 2020 07:49:12 GMT

←Older revision		Revision as of 07:49, 29 April 2020
Line 1:		Line 1:

	==Photoconverted red fluorescent protein DendRFP==		==Photoconverted red fluorescent protein DendRFP==
-	<StructureSection load='5exc' size='340' side='right' caption='[[5exc]], [[Resolution\|resolution]] 2.14Å' scene=''>	+	<StructureSection load='5exc' size='340' side='right'caption='[[5exc]], [[Resolution\|resolution]] 2.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EXC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Dendronephthya_sp._ssal-2002 Dendronephthya sp. ssal-2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EXC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=GOL:GLYCEROL'>GOL</scene>, <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=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [http://pdbe.org/5exc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [http://www.ebi.ac.uk/pdbsum/5exc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [http://pdbe.org/5exc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [http://www.ebi.ac.uk/pdbsum/5exc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5exc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5exc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dendronephthya sp. ssal-2002]]
		+	[[Category: Large Structures]]
	[[Category: Pletnev, S V]]		[[Category: Pletnev, S V]]
	[[Category: Pletnev, V Z]]		[[Category: Pletnev, V Z]]

OCA at 05:38, 9 September 2016

OCA — Fri, 09 Sep 2016 05:38:23 GMT

←Older revision		Revision as of 05:38, 9 September 2016
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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [http://pdbe.org/5exc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [http://www.ebi.ac.uk/pdbsum/5exc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [http://pdbe.org/5exc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [http://www.ebi.ac.uk/pdbsum/5exc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The fluorescent protein from Dendronephthya sp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of DendFP irreversibly changes from green (506 nm) to red (578 nm). The photoconversion is accompanied by cleavage of the peptide backbone at the C(alpha)-N bond of His62 and the formation of a terminal carboxamide group at the preceding Leu61. The resulting double C(alpha)=C(beta) bond in His62 extends the conjugation of the chromophore pi system to include imidazole, providing the red fluorescence. Here, the three-dimensional structures of native green and photoconverted red forms of DendFP determined at 1.81 and 2.14 A resolution, respectively, are reported. This is the first structure of photoconverted red DendFP to be reported to date. The structure-based mutagenesis of DendFP revealed an important role of positions 142 and 193: replacement of the original Ser142 and His193 caused a moderate red shift in the fluorescence and a considerable increase in the photoconversion rate. It was demonstrated that hydrogen bonding of the chromophore to the Gln116 and Ser105 cluster is crucial for variation of the photoconversion rate. The single replacement Gln116Asn disrupts the hydrogen bonding of Gln116 to the chromophore, resulting in a 30-fold decrease in the photoconversion rate, which was partially restored by a further Ser105Asn replacement.
		+
		+	Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms.,Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ Acta Crystallogr D Struct Biol. 2016 Aug;72(Pt 8):922-32. doi:, 10.1107/S205979831601038X. Epub 2016 Jul 13. PMID:27487823<ref>PMID:27487823</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5exc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:13, 4 August 2016

OCA — Thu, 04 Aug 2016 04:13:54 GMT

←Older revision		Revision as of 04:13, 4 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5exc is ~~ON HOLD~~	+	==Photoconverted red fluorescent protein DendRFP==
-		+	<StructureSection load='5exc' size='340' side='right' caption='[[5exc]], [[Resolution\|resolution]] 2.14Å' scene=''>
-	~~Authors~~: ~~Pletnev~~, V.Z., ~~Pletneva~~, N.V., ~~Pletnev~~, S.V.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5exc]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EXC FirstGlance]. <br>
-	~~Description: Photoconverted red fluorescent protein DendRFP~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NLW:L-LEUCINAMIDE'>NLW</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></td></tr>
-	[[Category: Pletnev, V.Z]]	+	<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=5exc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5exc OCA], [http://pdbe.org/5exc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5exc RCSB], [http://www.ebi.ac.uk/pdbsum/5exc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5exc ProSAT]</span></td></tr>
-	[[Category: Pletneva, N.V]]	+	</table>
-	[[Category: ~~Pletnev, S.V~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Pletnev, S V]]
		+	[[Category: Pletnev, V Z]]
		+	[[Category: Pletneva, N V]]
		+	[[Category: Beta-barrel]]
		+	[[Category: Biomarker]]
		+	[[Category: Chromophore]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Photoswitchable fluorescent protein]]

OCA: Protected "5exc" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2015 15:06:56 GMT

Protected "5exc" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:06, 2 December 2015

OCA: New page: '''Unreleased structure''' The entry 5exc is ON HOLD Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V. Description: Photoconverted red fluorescent protein DendRFP [[Category: Unrel...

OCA — Wed, 02 Dec 2015 15:06:54 GMT

New page: '''Unreleased structure''' The entry 5exc is ON HOLD Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V. Description: Photoconverted red fluorescent protein DendRFP [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 5exc is ON HOLD

Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.

Description: Photoconverted red fluorescent protein DendRFP
[[Category: Unreleased Structures]]
[[Category: Pletnev, V.Z]]
[[Category: Pletneva, N.V]]
[[Category: Pletnev, S.V]]