6t3l - Revision history

OCA at 16:06, 13 December 2023

OCA — Wed, 13 Dec 2023 16:06:20 GMT

←Older revision		Revision as of 16:06, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='6t3l' size='340' side='right'caption='[[6t3l]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='6t3l' size='340' side='right'caption='[[6t3l]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6t3l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T3L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6T3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t3l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T3L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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~~></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]] 2.07Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></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=6t3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t3l OCA], [~~http~~://pdbe.org/6t3l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6t3l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6t3l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6t3l 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=6t3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t3l OCA], [https://pdbe.org/6t3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t3l RCSB], [https://www.ebi.ac.uk/pdbsum/6t3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t3l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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.	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histidine kinase~~]]	+	[[Category: Deinococcus radiodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Claesson, E]]	+	[[Category: Claesson E]]
-	[[Category: Pandey, S]]	+	[[Category: Pandey S]]
-	[[Category: Schmidt, M]]	+	[[Category: Schmidt M]]
-	[[Category: Takala, H]]	+	[[Category: Takala H]]
-	~~[[Category: Wahlgren, W Yuan~~]]	+	[[Category: Westenhoff S]]
-	[[Category: Westenhoff, S]]	+	[[Category: Yuan Wahlgren W]]
-	[[Category: ~~Kinase]]~~	+
-	~~[[Category: Photosensor]]~~	+
-	~~[[Category: Phytochrome]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:54, 8 April 2020

OCA — Wed, 08 Apr 2020 06:54:51 GMT

←Older revision		Revision as of 06:54, 8 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6t3l is ~~ON HOLD~~	+	==PAS-GAF fragment from Deinococcus radiodurans phytochrome in dark state==
		+	<StructureSection load='6t3l' size='340' side='right'caption='[[6t3l]], [[Resolution\|resolution]] 2.07Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6t3l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T3L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T3L FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=6t3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t3l OCA], [http://pdbe.org/6t3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t3l RCSB], [http://www.ebi.ac.uk/pdbsum/6t3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t3l ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signalling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

-	~~Authors: Claesson~~, E., ~~Takala~~, H., ~~Yuan Wahlgren~~, W., ~~Pandey~~, S., ~~Schmidt~~, M., Westenhoff, S.	+	The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.,Claesson E, Wahlgren WY, Takala H, Pandey S, Castillon L, Kuznetsova V, Henry L, Panman M, Carrillo M, Kubel J, Nanekar R, Isaksson L, Nimmrich A, Cellini A, Morozov D, Maj M, Kurttila M, Bosman R, Nango E, Tanaka R, Tanaka T, Fangjia L, Iwata S, Owada S, Moffat K, Groenhof G, A Stojkovic E, A Ihalainen J, Schmidt M, Westenhoff S Elife. 2020 Mar 31;9. pii: 53514. doi: 10.7554/eLife.53514. PMID:32228856<ref>PMID:32228856</ref>

-	~~Description: PAS~~-~~GAF fragment from Deinococcus radiodurans phytochrome in dark state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Takala, H~~]]	+	<div class="pdbe-citations 6t3l" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Westenhoff, S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histidine kinase]]
		+	[[Category: Large Structures]]
	[[Category: Claesson, E]]		[[Category: Claesson, E]]
-	[[Category: Schmidt, M]]
-	[[Category: Yuan Wahlgren, W]]
	[[Category: Pandey, S]]		[[Category: Pandey, S]]
		+	[[Category: Schmidt, M]]
		+	[[Category: Takala, H]]
		+	[[Category: Wahlgren, W Yuan]]
		+	[[Category: Westenhoff, S]]
		+	[[Category: Kinase]]
		+	[[Category: Photosensor]]
		+	[[Category: Phytochrome]]
		+	[[Category: Transferase]]

OCA: Protected "6t3l" [edit=sysop:move=sysop]

OCA — Wed, 16 Oct 2019 04:32:22 GMT

Protected "6t3l" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:32, 16 October 2019

OCA: New page: '''Unreleased structure''' The entry 6t3l is ON HOLD Authors: Claesson, E., Takala, H., Yuan Wahlgren, W., Pandey, S., Schmidt, M., Westenhoff, S. Description: PAS-GAF fragment from De...

OCA — Wed, 16 Oct 2019 04:32:21 GMT

New page: '''Unreleased structure''' The entry 6t3l is ON HOLD Authors: Claesson, E., Takala, H., Yuan Wahlgren, W., Pandey, S., Schmidt, M., Westenhoff, S. Description: PAS-GAF fragment from De...

New page

'''Unreleased structure'''

The entry 6t3l is ON HOLD

Authors: Claesson, E., Takala, H., Yuan Wahlgren, W., Pandey, S., Schmidt, M., Westenhoff, S.

Description: PAS-GAF fragment from Deinococcus radiodurans phytochrome in dark state
[[Category: Unreleased Structures]]
[[Category: Takala, H]]
[[Category: Westenhoff, S]]
[[Category: Claesson, E]]
[[Category: Schmidt, M]]
[[Category: Yuan Wahlgren, W]]
[[Category: Pandey, S]]