6i23 - Revision history

OCA at 11:44, 24 January 2024

2024-01-24T11:44:52Z

←Older revision		Revision as of 11:44, 24 January 2024
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	<StructureSection load='6i23' size='340' side='right'caption='[[6i23]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6i23' size='340' side='right'caption='[[6i23]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i23]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Golden_alga Golden alga~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I23 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ochromonas_danica Ochromonas danica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I23 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OdAUREO1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2986 Golden alga])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=6i23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i23 OCA], [~~http~~://pdbe.org/6i23 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i23 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i23 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i23 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=6i23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i23 OCA], [https://pdbe.org/6i23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i23 RCSB], [https://www.ebi.ac.uk/pdbsum/6i23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i23 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C5NSW6_OCHDN C5NSW6_OCHDN]
	<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: Golden alga]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Allemann, R K~~]]	+	[[Category: Ochromonas danica]]
-	[[Category: ~~Johnson, L A~~]]	+	[[Category: Allemann RK]]
-	[[Category: ~~Kalvaitis, M E~~]]	+	[[Category: Johnson LA]]
-	[[Category: ~~Mart, R J~~]]	+	[[Category: Kalvaitis ME]]
-	[[Category: ~~Rizkallah, P J~~]]	+	[[Category: Mart RJ]]
-	[[Category: ~~Dark grown]]~~	+	[[Category: Rizkallah PJ]]
-	~~[[Category: Fluorescence]]~~	+
-	~~[[Category: Fmn]]~~	+
-	~~[[Category: Light sensing]]~~	+
-	~~[[Category: Lov domain]]~~	+
-	~~[[Category: Ochronomas danica]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor pas domain~~]]	+

OCA at 06:29, 19 June 2019

2019-06-19T06:29:13Z

←Older revision		Revision as of 06:29, 19 June 2019
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	<StructureSection load='6i23' size='340' side='right'caption='[[6i23]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6i23' size='340' side='right'caption='[[6i23]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i23]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Golden_alga Golden alga]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I23 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OdAUREO1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2986 Golden alga])</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=6i23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i23 OCA], [http://pdbe.org/6i23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i23 RCSB], [http://www.ebi.ac.uk/pdbsum/6i23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i23 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=6i23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i23 OCA], [http://pdbe.org/6i23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i23 RCSB], [http://www.ebi.ac.uk/pdbsum/6i23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i23 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Golden alga]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Allemann, R K]]		[[Category: Allemann, R K]]

OCA at 06:08, 29 May 2019

2019-05-29T06:08:37Z

←Older revision		Revision as of 06:08, 29 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i23 is ~~ON HOLD until Paper~~ Publication	+	==Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism==
		+	<StructureSection load='6i23' size='340' side='right'caption='[[6i23]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i23]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I23 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O9:1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol'>9O9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=6i23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i23 OCA], [http://pdbe.org/6i23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i23 RCSB], [http://www.ebi.ac.uk/pdbsum/6i23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i23 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Light-oxygen-voltage (LOV) domains are increasingly used to engineer photoresponsive biological systems. While the photochemical cycle is well documented, the allosteric mechanism by which formation of a cysteinyl-flavin adduct leads to activation is unclear. Via replacement of flavin mononucleotide (FMN) with 5-deazaflavin mononucleotide (5dFMN) in the Aureochrome1a (Au1a) transcription factor from Ochromonas danica, a thermally stable cysteinyl-5dFMN adduct was generated. High-resolution crystal structures (<2 A) under different illumination conditions with either FMN or 5dFMN chromophores reveal three conformations of the highly conserved glutamine 293. An allosteric hydrogen bond network linking the chromophore via Gln293 to the auxiliary A'alpha helix is observed. With FMN, a "flip" of the Gln293 side chain occurs between dark and lit states. 5dFMN cannot hydrogen bond through the C5 position and proved to be unable to support Au1a domain dimerization. Under blue light, the Gln293 side chain instead "swings" away in a conformation distal to the chromophore and not previously observed in existing LOV domain structures. Together, the multiple side chain conformations of Gln293 and functional analysis of 5dFMN provide new insight into the structural requirements for LOV domain activation.

-	~~Authors~~:	+	A Noncanonical Chromophore Reveals Structural Rearrangements of the Light-Oxygen-Voltage Domain upon Photoactivation.,Kalvaitis ME, Johnson LA, Mart RJ, Rizkallah P, Allemann RK Biochemistry. 2019 May 17. doi: 10.1021/acs.biochem.9b00255. PMID:31082213<ref>PMID:31082213</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6i23" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Allemann, R K]]
		+	[[Category: Johnson, L A]]
		+	[[Category: Kalvaitis, M E]]
		+	[[Category: Mart, R J]]
		+	[[Category: Rizkallah, P J]]
		+	[[Category: Dark grown]]
		+	[[Category: Fluorescence]]
		+	[[Category: Fmn]]
		+	[[Category: Light sensing]]
		+	[[Category: Lov domain]]
		+	[[Category: Ochronomas danica]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor pas domain]]

OCA at 06:18, 14 November 2018

2018-11-14T06:18:14Z

←Older revision		Revision as of 06:18, 14 November 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i23 is ON HOLD until ~~sometime in the future~~	+	The entry 6i23 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6i23" [edit=sysop:move=sysop]

2018-11-07T10:38:51Z

Protected "6i23" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:38, 7 November 2018

OCA: New page: '''Unreleased structure''' The entry 6i23 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

2018-11-07T10:38:49Z

New page: '''Unreleased structure''' The entry 6i23 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6i23 is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]