6jgj - Revision history

OCA at 10:27, 15 November 2023

2023-11-15T10:27:41Z

←Older revision		Revision as of 10:27, 15 November 2023
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	<StructureSection load='6jgj' size='340' side='right'caption='[[6jgj]], [[Resolution\|resolution]] 0.78Å' scene=''>		<StructureSection load='6jgj' size='340' side='right'caption='[[6jgj]], [[Resolution\|resolution]] 0.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jgj]] 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=6JGJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jgj]] 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=6JGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JGJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</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]] 0.78Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6jgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgj OCA], [https://pdbe.org/6jgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jgj RCSB], [https://www.ebi.ac.uk/pdbsum/6jgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgj 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=6jgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgj OCA], [~~http~~://pdbe.org/6jgj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jgj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jgj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgj 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6jgj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jgj" 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: ~~Aeqvi~~]]	+	[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hanazono, Y]]	+	[[Category: Hanazono Y]]
-	[[Category: Miki, K]]	+	[[Category: Miki K]]
-	[[Category: Tai, Y]]	+	[[Category: Tai Y]]
-	[[Category: Takaba, K]]	+	[[Category: Takaba K]]
-	[[Category: Takeda, K]]	+	[[Category: Takeda K]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Green fluorescent protein]]~~	+
-	~~[[Category: Hydrogen~~]]	+

OCA at 06:36, 29 May 2019

2019-05-29T06:36:42Z

←Older revision		Revision as of 06:36, 29 May 2019
Line 11:		Line 11:
	== 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.		[[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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-pi interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.
		+
		+	Subatomic resolution X-ray structures of green fluorescent protein.,Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K, Takeda K IUCrJ. 2019 Apr 3;6(Pt 3):387-400. doi: 10.1107/S205225251900246X. eCollection, 2019 May 1. PMID:31098020<ref>PMID:31098020</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jgj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:17, 1 May 2019

2019-05-01T09:17:14Z

←Older revision		Revision as of 09:17, 1 May 2019
Line 3:		Line 3:
	<StructureSection load='6jgj' size='340' side='right'caption='[[6jgj]], [[Resolution\|resolution]] 0.78Å' scene=''>		<StructureSection load='6jgj' size='340' side='right'caption='[[6jgj]], [[Resolution\|resolution]] 0.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jgj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jgj]] 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=6JGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JGJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><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=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></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=6jgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgj OCA], [http://pdbe.org/6jgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jgj RCSB], [http://www.ebi.ac.uk/pdbsum/6jgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgj 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=6jgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgj OCA], [http://pdbe.org/6jgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jgj RCSB], [http://www.ebi.ac.uk/pdbsum/6jgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgj ProSAT]</span></td></tr>
	</table>		</table>
Line 12:		Line 13:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeqvi]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hanazono, Y]]		[[Category: Hanazono, Y]]

OCA at 06:00, 17 April 2019

2019-04-17T06:00:44Z

←Older revision		Revision as of 06:00, 17 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jgj is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A==
-		+	<StructureSection load='6jgj' size='340' side='right'caption='[[6jgj]], [[Resolution\|resolution]] 0.78Å' scene=''>
-	~~Authors~~: ~~Takaba~~, K., ~~Tai~~, Y., ~~Hanazono, Y~~.~~, Miki, K~~., ~~Takeda~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jgj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JGJ FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the F99S~~/~~M153T~~/~~V163A~~/~~E222Q variant~~ of ~~GFP at 0~~.~~78 A~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></td></tr>
-	[[Category: ~~Takeda~~, K]]	+	<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=6jgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgj OCA], [http://pdbe.org/6jgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jgj RCSB], [http://www.ebi.ac.uk/pdbsum/6jgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgj ProSAT]</span></td></tr>
		+	</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.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hanazono, Y]]
		+	[[Category: Miki, K]]
	[[Category: Tai, Y]]		[[Category: Tai, Y]]
	[[Category: Takaba, K]]		[[Category: Takaba, K]]
-	[[Category: ~~Hanazono~~, Y]]	+	[[Category: Takeda, K]]
-	[[Category: ~~Miki, K~~]]	+	[[Category: Fluorescent protein]]
		+	[[Category: Green fluorescent protein]]
		+	[[Category: Hydrogen]]

OCA at 05:48, 20 March 2019

2019-03-20T05:48:43Z

←Older revision		Revision as of 05:48, 20 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jgj is ON HOLD	+	The entry 6jgj is ON HOLD until Paper Publication

	Authors: Takaba, K., Tai, Y., Hanazono, Y., Miki, K., Takeda, K.		Authors: Takaba, K., Tai, Y., Hanazono, Y., Miki, K., Takeda, K.

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

2019-02-21T05:00:53Z

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

←Older revision

Revision as of 05:00, 21 February 2019

OCA: New page: '''Unreleased structure''' The entry 6jgj is ON HOLD Authors: Takaba, K., Tai, Y., Hanazono, Y., Miki, K., Takeda, K. Description: Crystal structure of the F99S/M153T/V163A/E222Q varia...

2019-02-21T05:00:52Z

New page: '''Unreleased structure''' The entry 6jgj is ON HOLD Authors: Takaba, K., Tai, Y., Hanazono, Y., Miki, K., Takeda, K. Description: Crystal structure of the F99S/M153T/V163A/E222Q varia...

New page

'''Unreleased structure'''

The entry 6jgj is ON HOLD

Authors: Takaba, K., Tai, Y., Hanazono, Y., Miki, K., Takeda, K.

Description: Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A
[[Category: Unreleased Structures]]
[[Category: Takeda, K]]
[[Category: Tai, Y]]
[[Category: Takaba, K]]
[[Category: Hanazono, Y]]
[[Category: Miki, K]]