6ofk - Revision history

OCA at 09:15, 25 October 2023

OCA — Wed, 25 Oct 2023 09:15:47 GMT

←Older revision		Revision as of 09:15, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OFK FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OFK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</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]] 1.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [https://pdbe.org/6ofk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [https://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk 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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [https://pdbe.org/6ofk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [https://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:31, 15 February 2023

OCA — Wed, 15 Feb 2023 10:31:59 GMT

←Older revision		Revision as of 10:31, 15 February 2023
Line 3:		Line 3:
	<StructureSection load='6ofk' size='340' side='right'caption='[[6ofk]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='6ofk' size='340' side='right'caption='[[6ofk]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aeqvi Aeqvi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OFK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [~~http~~://pdbe.org/6ofk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk 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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [https://pdbe.org/6ofk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [https://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk ProSAT]</span></td></tr>
	</table>		</table>
		+	== 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aeqvi~~]]	+	[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boxer~~, S G~~]]	+	[[Category: Boxer SG]]
-	[[Category: Lin, C Y]]	+	[[Category: Lin C-Y]]
-	[[Category: Mathews~~, I I~~]]	+	[[Category: Mathews II]]
-	[[Category: Romei~~, M G]]~~	+	[[Category: Romei MG]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Gfp~~]]	+

OCA at 11:14, 2 October 2019

OCA — Wed, 02 Oct 2019 11:14:55 GMT

←Older revision		Revision as of 11:14, 2 October 2019
Line 3:		Line 3:
	<StructureSection load='6ofk' size='340' side='right'caption='[[6ofk]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='6ofk' size='340' side='right'caption='[[6ofk]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OFK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [http://pdbe.org/6ofk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [http://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk 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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [http://pdbe.org/6ofk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [http://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
		+
		+	Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins.,Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG J Am Chem Soc. 2019 Sep 25;141(38):15250-15265. doi: 10.1021/jacs.9b07152. Epub, 2019 Sep 11. PMID:31450887<ref>PMID:31450887</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ofk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeqvi]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Boxer, S G]]		[[Category: Boxer, S G]]

OCA at 05:49, 10 July 2019

OCA — Wed, 10 Jul 2019 05:49:56 GMT

←Older revision		Revision as of 05:49, 10 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ofk ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of green fluorescent protein (GFP); S65T; ih circular permutant (50-51)==
-		+	<StructureSection load='6ofk' size='340' side='right'caption='[[6ofk]], [[Resolution\|resolution]] 1.15Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ofk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OFK FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6ofk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ofk OCA], [http://pdbe.org/6ofk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ofk RCSB], [http://www.ebi.ac.uk/pdbsum/6ofk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ofk ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Boxer, S G]]
		+	[[Category: Lin, C Y]]
		+	[[Category: Mathews, I I]]
		+	[[Category: Romei, M G]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Gfp]]

OCA: Protected "6ofk" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2019 05:31:10 GMT

Protected "6ofk" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6ofk is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Apr 2019 05:31:09 GMT

New page: '''Unreleased structure''' The entry 6ofk is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ofk is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]