5h87 - Revision history

OCA at 07:26, 9 August 2023

2023-08-09T07:26:58Z

←Older revision		Revision as of 07:26, 9 August 2023
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	<StructureSection load='5h87' size='340' side='right'caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='5h87' size='340' side='right'caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h87]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dissp Dissp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H87 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5H87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h87]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H87 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</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]] 2.24Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h88\|5h88]], [[5h89\|5h89]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAmCherry ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86600 DISSP])~~</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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [https://pdbe.org/5h87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [https://www.ebi.ac.uk/pdbsum/5h87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h87 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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [~~http~~://pdbe.org/5h87 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h87 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h87 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1MPT3_DISSP D1MPT3_DISSP]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dissp~~]]	+	[[Category: Discosoma sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chica~~, R A~~]]	+	[[Category: Chica RA]]
-	[[Category: Couture, J F]]	+	[[Category: Couture J-F]]
-	[[Category: Pandelieva~~, A T~~]]	+	[[Category: Pandelieva AT]]
-	[[Category: Sarvan, S]]	+	[[Category: Sarvan S]]
-	[[Category: Tremblay, V]]	+	[[Category: Tremblay V]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: Quantum yield~~]]	+

OCA at 06:55, 20 May 2020

2020-05-20T06:55:02Z

←Older revision		Revision as of 06:55, 20 May 2020
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	==Crystal structure of mRojoA mutant - P63H - W143S==		==Crystal structure of mRojoA mutant - P63H - W143S==
-	<StructureSection load='5h87' size='340' side='right' caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='5h87' size='340' side='right'caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h87]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H87 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dissp Dissp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H87 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H87 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</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=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h88\|5h88]], [[5h89\|5h89]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h88\|5h88]], [[5h89\|5h89]]</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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [http://pdbe.org/5h87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [http://www.ebi.ac.uk/pdbsum/5h87 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAmCherry ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86600 DISSP])</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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [http://pdbe.org/5h87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [http://www.ebi.ac.uk/pdbsum/5h87 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h87 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dissp]]
		+	[[Category: Large Structures]]
	[[Category: Chica, R A]]		[[Category: Chica, R A]]
	[[Category: Couture, J F]]		[[Category: Couture, J F]]

OCA at 06:55, 2 March 2016

2016-03-02T06:55:38Z

←Older revision		Revision as of 06:55, 2 March 2016
Line 1:		Line 1:
		+
	==Crystal structure of mRojoA mutant - P63H - W143S==		==Crystal structure of mRojoA mutant - P63H - W143S==
	<StructureSection load='5h87' size='340' side='right' caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='5h87' size='340' side='right' caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>

OCA at 07:46, 3 February 2016

2016-02-03T07:46:53Z

←Older revision		Revision as of 07:46, 3 February 2016
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	<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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [http://pdbe.org/5h87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [http://www.ebi.ac.uk/pdbsum/5h87 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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [http://pdbe.org/5h87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [http://www.ebi.ac.uk/pdbsum/5h87 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Red fluorescent proteins (RFPs) are used extensively in chemical biology research as fluorophores for live cell imaging, as partners in FRET pairs, and as signal transducers in biosensors. For all of these applications, brighter RFP variants are desired. Here, we used rational design to increase the quantum yield of monomeric RFPs in order to improve their brightness. We postulated that we could increase quantum yield by restricting the conformational degrees of freedom of the RFP chromophore. To test our hypothesis, we introduced aromatic residues above the chromophore of mRojoA, a dim RFP containing a pi-stacked Tyr residue directly beneath the chromophore, in order to reduce chromophore conformational flexibility via improved packing and steric complementarity. The best mutant identified displayed an absolute quantum yield increase of 0.07, representing an over 3-fold improvement relative to mRojoA. Remarkably, this variant was isolated following the screening of only 48 mutants, a library size that is several orders of magnitude smaller than those previously used to achieve equivalent gains in quantum yield in other RFPs. The crystal structure of the highest quantum yield mutant showed that the chromophore is sandwiched between two Tyr residues in a triple-decker motif of aromatic rings. Presence of this motif increases chromophore rigidity, as evidenced by the significantly reduced temperature factors compared to dim RFPs. Overall, the approach presented here paves the way for the rapid development of fluorescent proteins with higher quantum yield and overall brightness.
		+
		+	Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif.,Pandelieva AT, Baran MJ, Calderini GF, McCann JL, Tremblay V, Sarvan S, Davey JA, Couture JF, Chica RA ACS Chem Biol. 2016 Jan 5. PMID:26697759<ref>PMID:26697759</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5h87" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:39, 28 January 2016

2016-01-28T02:39:18Z

←Older revision		Revision as of 02:39, 28 January 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of mRojoA mutant - P63H - W143S==
-		+	<StructureSection load='5h87' size='340' side='right' caption='[[5h87]], [[Resolution\|resolution]] 2.24Å' scene=''>
-	~~The entry~~ 5h87 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5h87]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H87 FirstGlance]. <br>
-	~~Authors~~: ~~Pandelieva~~, A.T., ~~Tremblay, V~~., ~~Sarvan, S~~., ~~Chica, R~~.A., ~~Couture, J~~.-F.	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h88\|5h88]], [[5h89\|5h89]]</td></tr>
-	~~Description: Crystal structure of mRojoA mutant -P63H -W143S~~	+	<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=5h87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h87 OCA], [http://pdbe.org/5h87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h87 RCSB], [http://www.ebi.ac.uk/pdbsum/5h87 PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Couture, J.-F]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Chica, R A]]
		+	[[Category: Couture, J F]]
		+	[[Category: Pandelieva, A T]]
	[[Category: Sarvan, S]]		[[Category: Sarvan, S]]
-	[[Category: Chica, R.A]]
-	[[Category: Pandelieva, A.T]]
	[[Category: Tremblay, V]]		[[Category: Tremblay, V]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Protein engineering]]
		+	[[Category: Quantum yield]]

OCA: Protected "5h87" [edit=sysop:move=sysop]

2015-12-30T18:22:48Z

Protected "5h87" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:22, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5h87 is ON HOLD Authors: Pandelieva, A.T., Tremblay, V., Sarvan, S., Chica, R.A., Couture, J.-F. Description: Crystal structure of mRojoA mutant -P...

2015-12-30T18:22:46Z

New page: '''Unreleased structure''' The entry 5h87 is ON HOLD Authors: Pandelieva, A.T., Tremblay, V., Sarvan, S., Chica, R.A., Couture, J.-F. Description: Crystal structure of mRojoA mutant -P...

New page

'''Unreleased structure'''

The entry 5h87 is ON HOLD

Authors: Pandelieva, A.T., Tremblay, V., Sarvan, S., Chica, R.A., Couture, J.-F.

Description: Crystal structure of mRojoA mutant -P63H -W143S
[[Category: Unreleased Structures]]
[[Category: Couture, J.-F]]
[[Category: Sarvan, S]]
[[Category: Chica, R.A]]
[[Category: Pandelieva, A.T]]
[[Category: Tremblay, V]]