6r26 - Revision history

OCA at 12:13, 24 January 2024

OCA — Wed, 24 Jan 2024 12:13:28 GMT

←Older revision		Revision as of 12:13, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6r26' size='340' side='right'caption='[[6r26]], [[Resolution\|resolution]] 3.11Å' scene=''>		<StructureSection load='6r26' size='340' side='right'caption='[[6r26]], [[Resolution\|resolution]] 3.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r26]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R26 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R26 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r26]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R26 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=JQ2:3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3,7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic+acid'>JQ2</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]] 3.11Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=JQ2:3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3,7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic+acid'>JQ2</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i5l\|5i5l]], [[5hsq\|5hsq]], [[6r27\|6r27]]~~</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=6r26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r26 OCA], [https://pdbe.org/6r26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r26 RCSB], [https://www.ebi.ac.uk/pdbsum/6r26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r26 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=6r26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r26 OCA], [~~http~~://pdbe.org/6r26 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r26 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r26 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r26 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q7CY45_AGRFC Q7CY45_AGRFC]
-	Phytochromes are photochromic photoreceptors with a bilin chromophore that have been found in plants and bacteria. Typical bacterial phytochromes are composed of an N-terminal photosensory chromophore module and a C-terminal protein kinase. The former contains the chromophore, which allows phytochromes to adopt the two interconvertible spectral forms, Pr and Pfr. The N-terminal photosensory module of Agrobacterium phytochrome Agp1, Agp1-M15, was used for crystallization studies. The protein was either assembled with the natural chromophore biliverdin or a sterically locked synthetic biliverdin-derivative, termed 15Za. The last-named adduct does not undergo photoisomerization due to an additional carbon chain between the rings C and D of the chromophore. Both adducts could be crystallized, but the resolution was largely improved by the use of 15Za. Crystals of biliverdin-Agp1-M15 diffract to 6A resolution and belong to the tetragonal space group I422 with unit cell dimensions a = b = 171 Angstroms, c = 81 Angstroms, crystals of 15Za-Agp1-M15 belong to the same space group with similar unit cell dimensions a = b = 174 Angstroms, c = 80 Angstroms, but diffract to 3.4 Angstroms resolution. Assuming the asymmetric unit to be occupied by one monomer of 55kDa, the unit cell contains 54-55% solvent with a crystal volume per protein mass, V(m), of 2.7 Angstroms(3) Da(-1).	+
-		+
-	Crystallization and preliminary X-ray crystallographic analysis of the N-terminal photosensory module of phytochrome Agp1, a biliverdin-binding photoreceptor from Agrobacterium tumefaciens.,Scheerer P, Michael N, Park JH, Noack S, Forster C, Hammam MA, Inomata K, Choe HW, Lamparter T, Krauss N J Struct Biol. 2006 Jan;153(1):~~97-102. doi: 10.1016~~/~~j.jsb.2005.11.002. Epub 2005 , Dec 1. PMID:16377207<ref>PMID:16377207<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6r26" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrobacterium fabrum str. C58]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Krauss, N]]	+	[[Category: Krauss N]]
-	[[Category: Lamparter, T]]	+	[[Category: Lamparter T]]
-	[[Category: Michael, N]]	+	[[Category: Michael N]]
-	[[Category: Scheerer, P]]	+	[[Category: Scheerer P]]
-	~~[[Category: Bilin protein]]~~	+
-	~~[[Category: Crystallographic superstructure]]~~	+
-	~~[[Category: Locked chromophore]]~~	+
-	~~[[Category: Photoreceptor]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 09:19, 1 April 2020

OCA — Wed, 01 Apr 2020 09:19:17 GMT

←Older revision		Revision as of 09:19, 1 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6r26 is ~~ON HOLD until Paper~~ Publication	+	==The photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state==
		+	<StructureSection load='6r26' size='340' side='right'caption='[[6r26]], [[Resolution\|resolution]] 3.11Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r26]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R26 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=JQ2:3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3,7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic+acid'>JQ2</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i5l\|5i5l]], [[5hsq\|5hsq]], [[6r27\|6r27]]</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=6r26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r26 OCA], [http://pdbe.org/6r26 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r26 RCSB], [http://www.ebi.ac.uk/pdbsum/6r26 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r26 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phytochromes are photochromic photoreceptors with a bilin chromophore that have been found in plants and bacteria. Typical bacterial phytochromes are composed of an N-terminal photosensory chromophore module and a C-terminal protein kinase. The former contains the chromophore, which allows phytochromes to adopt the two interconvertible spectral forms, Pr and Pfr. The N-terminal photosensory module of Agrobacterium phytochrome Agp1, Agp1-M15, was used for crystallization studies. The protein was either assembled with the natural chromophore biliverdin or a sterically locked synthetic biliverdin-derivative, termed 15Za. The last-named adduct does not undergo photoisomerization due to an additional carbon chain between the rings C and D of the chromophore. Both adducts could be crystallized, but the resolution was largely improved by the use of 15Za. Crystals of biliverdin-Agp1-M15 diffract to 6A resolution and belong to the tetragonal space group I422 with unit cell dimensions a = b = 171 Angstroms, c = 81 Angstroms, crystals of 15Za-Agp1-M15 belong to the same space group with similar unit cell dimensions a = b = 174 Angstroms, c = 80 Angstroms, but diffract to 3.4 Angstroms resolution. Assuming the asymmetric unit to be occupied by one monomer of 55kDa, the unit cell contains 54-55% solvent with a crystal volume per protein mass, V(m), of 2.7 Angstroms(3) Da(-1).

-	~~Authors: Scheerer~~, P., ~~Michael~~, N., ~~Lamparter~~, T., Krauss, N.	+	Crystallization and preliminary X-ray crystallographic analysis of the N-terminal photosensory module of phytochrome Agp1, a biliverdin-binding photoreceptor from Agrobacterium tumefaciens.,Scheerer P, Michael N, Park JH, Noack S, Forster C, Hammam MA, Inomata K, Choe HW, Lamparter T, Krauss N J Struct Biol. 2006 Jan;153(1):97-102. doi: 10.1016/j.jsb.2005.11.002. Epub 2005 , Dec 1. PMID:16377207<ref>PMID:16377207</ref>

-	~~Description: The photosensory core module (PAS-GAF-PHY)~~ of the ~~bacterial phytochrome Agp1 (AtBphP1) locked in a Pr~~-~~like state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r26" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Krauss, N]]		[[Category: Krauss, N]]
-	[[Category: Scheerer, P]]
	[[Category: Lamparter, T]]		[[Category: Lamparter, T]]
	[[Category: Michael, N]]		[[Category: Michael, N]]
		+	[[Category: Scheerer, P]]
		+	[[Category: Bilin protein]]
		+	[[Category: Crystallographic superstructure]]
		+	[[Category: Locked chromophore]]
		+	[[Category: Photoreceptor]]
		+	[[Category: Signaling protein]]

OCA at 04:53, 3 April 2019

OCA — Wed, 03 Apr 2019 04:53:05 GMT

←Older revision		Revision as of 04:53, 3 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6r26 is ON HOLD	+	The entry 6r26 is ON HOLD until Paper Publication

	Authors: Scheerer, P., Michael, N., Lamparter, T., Krauss, N.		Authors: Scheerer, P., Michael, N., Lamparter, T., Krauss, N.

-	Description: ~~Crystallographic superstructure of the~~ photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state	+	Description: The photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Krauss, N]]		[[Category: Krauss, N]]

OCA: Protected "6r26" [edit=sysop:move=sysop]

OCA — Wed, 27 Mar 2019 05:12:00 GMT

Protected "6r26" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:12, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r26 is ON HOLD Authors: Scheerer, P., Michael, N., Lamparter, T., Krauss, N. Description: Crystallographic superstructure of the photosensory core...

OCA — Wed, 27 Mar 2019 05:11:59 GMT

New page: '''Unreleased structure''' The entry 6r26 is ON HOLD Authors: Scheerer, P., Michael, N., Lamparter, T., Krauss, N. Description: Crystallographic superstructure of the photosensory core...

New page

'''Unreleased structure'''

The entry 6r26 is ON HOLD

Authors: Scheerer, P., Michael, N., Lamparter, T., Krauss, N.

Description: Crystallographic superstructure of the photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state
[[Category: Unreleased Structures]]
[[Category: Krauss, N]]
[[Category: Scheerer, P]]
[[Category: Lamparter, T]]
[[Category: Michael, N]]