7z9d - Revision history

OCA at 13:30, 1 February 2024

OCA — Thu, 01 Feb 2024 13:30:04 GMT

←Older revision		Revision as of 13:30, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7z9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9D FirstGlance]. <br>		<table><tr><td colspan='2'>[[7z9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9D 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=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.88Å</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=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=7z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9d OCA], [https://pdbe.org/7z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9d RCSB], [https://www.ebi.ac.uk/pdbsum/7z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9d 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=7z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9d OCA], [https://pdbe.org/7z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9d RCSB], [https://www.ebi.ac.uk/pdbsum/7z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9d ProSAT]</span></td></tr>
	</table>		</table>

OCA at 20:29, 16 November 2022

OCA — Wed, 16 Nov 2022 20:29:03 GMT

←Older revision		Revision as of 20:29, 16 November 2022
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	==Deinococcus radiodurans BphP PAS-GAF H260A mutant==		==Deinococcus radiodurans BphP PAS-GAF H260A mutant==
-	<StructureSection load='7z9d' size='340' side='right'caption='[[7z9d]]' scene=''>	+	<StructureSection load='7z9d' size='340' side='right'caption='[[7z9d]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9D FirstGlance]. <br>
-	</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=7z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9d OCA], [https://pdbe.org/7z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9d RCSB], [https://www.ebi.ac.uk/pdbsum/7z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9d ProSAT]</span></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=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=7z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9d OCA], [https://pdbe.org/7z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9d RCSB], [https://www.ebi.ac.uk/pdbsum/7z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9d ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phytochromes are red light-sensing photoreceptor proteins that bind a bilin chromophore. Here, we investigate the role of a conserved histidine (H260) and tyrosine (Y263) in the chromophore-binding domain (CBD) of Deinococcus radiodurans phytochrome (DrBphP). Using crystallography, we show that in the H260A variant, the missing imidazole side chain leads to increased water content in the binding pocket. On the other hand, Y263F mutation reduces the water occupancy around the chromophore. Together, these changes in water coordination alter the protonation and spectroscopic properties of the biliverdin. These results pinpoint the importance of this conserved histidine and tyrosine, and the related water network, for the function and applications of phytochromes.
		+
		+	Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome.,Lehtivuori H, Rumfeldt J, Mustalahti S, Kurkinen S, Takala H Photochem Photobiol Sci. 2022 Jul 29. pii: 10.1007/s43630-022-00272-6. doi:, 10.1007/s43630-022-00272-6. PMID:35906527<ref>PMID:35906527</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z9d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Takala H]]		[[Category: Takala H]]

OCA at 05:03, 10 August 2022

OCA — Wed, 10 Aug 2022 05:03:05 GMT

←Older revision		Revision as of 05:03, 10 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7z9d ~~is ON HOLD until Paper Publication~~	+	==Deinococcus radiodurans BphP PAS-GAF H260A mutant==
-		+	<StructureSection load='7z9d' size='340' side='right'caption='[[7z9d]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9D FirstGlance]. <br>
-	~~Description~~:	+	</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=7z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9d OCA], [https://pdbe.org/7z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9d RCSB], [https://www.ebi.ac.uk/pdbsum/7z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9d ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Takala H]]

OCA at 08:45, 13 April 2022

OCA — Wed, 13 Apr 2022 08:45:58 GMT

←Older revision		Revision as of 08:45, 13 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7z9d is ON HOLD	+	The entry 7z9d is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7z9d" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2022 09:48:42 GMT

Protected "7z9d" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:48, 30 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z9d is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Mar 2022 09:48:41 GMT

New page: '''Unreleased structure''' The entry 7z9d is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7z9d is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]