5hsq - Revision history

OCA at 10:52, 16 August 2023

OCA — Wed, 16 Aug 2023 10:52:58 GMT

←Older revision		Revision as of 10:52, 16 August 2023
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	<StructureSection load='5hsq' size='340' side='right'caption='[[5hsq]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5hsq' size='340' side='right'caption='[[5hsq]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hsq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hsq]] 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=5HSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HSQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 1.85Å</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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [~~http~~://pdbe.org/5hsq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [https://pdbe.org/5hsq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [https://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q7CY45_AGRFC Q7CY45_AGRFC]
	<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: Agrobacterium fabrum str. C58]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Krauss, N]]	+	[[Category: Krauss N]]
-	[[Category: Lamparter, T]]	+	[[Category: Lamparter T]]
-	[[Category: Nagano, S]]	+	[[Category: Nagano S]]
-	[[Category: Scheerer, P]]	+	[[Category: Scheerer P]]
-	[[Category: Zubow, K]]	+	[[Category: Zubow K]]
-	~~[[Category: Bilin chromophore]]~~	+
-	~~[[Category: Photoisomerization]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Surface mutation~~]]	+

OCA at 08:30, 27 May 2020

OCA — Wed, 27 May 2020 08:30:41 GMT

←Older revision		Revision as of 08:30, 27 May 2020
Line 1:		Line 1:

	==The surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.==		==The surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.==
-	<StructureSection load='5hsq' size='340' side='right' caption='[[5hsq]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5hsq' size='340' side='right'caption='[[5hsq]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hsq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hsq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HSQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [http://pdbe.org/5hsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [http://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq ProSAT]</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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [http://pdbe.org/5hsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [http://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Krauss, N]]		[[Category: Krauss, N]]
	[[Category: Lamparter, T]]		[[Category: Lamparter, T]]

OCA at 08:42, 10 August 2016

OCA — Wed, 10 Aug 2016 08:42:22 GMT

←Older revision		Revision as of 08:42, 10 August 2016
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	<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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [http://pdbe.org/5hsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [http://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq 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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [http://pdbe.org/5hsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [http://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent Pr and Pfr states. These changes include secondary structure rearrangements in the so-called tongue of the PHY domain and structural rearrangements within the long alpha-helix that connects the GAF and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 A resolution and of a surface-engineered mutant of this PCM at 1.85 A resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting alpha-helix and the tongue, indicating pronounced structural flexibility which may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro461 of the conserved PRxSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.
		+
		+	The Crystal Structures of the N-Terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-Parallel Dimers.,Nagano S, Scheerer P, Zubow K, Michael N, Inomata K, Lamparter T, Krauss N J Biol Chem. 2016 Jul 26. pii: jbc.M116.739136. PMID:27466363<ref>PMID:27466363</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5hsq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:15, 4 August 2016

OCA — Thu, 04 Aug 2016 04:15:40 GMT

←Older revision		Revision as of 04:15, 4 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5hsq is ON HOLD until Paper Publication~~	+	==The surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.==
-		+	<StructureSection load='5hsq' size='340' side='right' caption='[[5hsq]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~Authors: Nagano, S., Scheerer, P., Zubow, K., Lamparter, T., Krauss, N.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5hsq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HSQ FirstGlance]. <br>
-	~~Description:~~ The surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsq OCA], [http://pdbe.org/5hsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsq RCSB], [http://www.ebi.ac.uk/pdbsum/5hsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsq ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Krauss, N]]		[[Category: Krauss, N]]
-	[[Category: Zubow, K]]
-	[[Category: Scheerer, P]]
	[[Category: Lamparter, T]]		[[Category: Lamparter, T]]
	[[Category: Nagano, S]]		[[Category: Nagano, S]]
		+	[[Category: Scheerer, P]]
		+	[[Category: Zubow, K]]
		+	[[Category: Bilin chromophore]]
		+	[[Category: Photoisomerization]]
		+	[[Category: Signaling protein]]
		+	[[Category: Surface mutation]]

OCA at 01:07, 21 February 2016

OCA — Sun, 21 Feb 2016 01:07:55 GMT

←Older revision		Revision as of 01:07, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hsq is ON HOLD	+	The entry 5hsq is ON HOLD until Paper Publication

	Authors: Nagano, S., Scheerer, P., Zubow, K., Lamparter, T., Krauss, N.		Authors: Nagano, S., Scheerer, P., Zubow, K., Lamparter, T., Krauss, N.

OCA: Protected "5hsq" [edit=sysop:move=sysop]

OCA — Wed, 03 Feb 2016 14:17:09 GMT

Protected "5hsq" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:17, 3 February 2016

OCA: New page: '''Unreleased structure''' The entry 5hsq is ON HOLD Authors: Nagano, S., Scheerer, P., Zubow, K., Lamparter, T., Krauss, N. Description: The surface engineered photosensory module (PA...

OCA — Wed, 03 Feb 2016 14:17:07 GMT

New page: '''Unreleased structure''' The entry 5hsq is ON HOLD Authors: Nagano, S., Scheerer, P., Zubow, K., Lamparter, T., Krauss, N. Description: The surface engineered photosensory module (PA...

New page

'''Unreleased structure'''

The entry 5hsq is ON HOLD

Authors: Nagano, S., Scheerer, P., Zubow, K., Lamparter, T., Krauss, N.

Description: The surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.
[[Category: Unreleased Structures]]
[[Category: Krauss, N]]
[[Category: Zubow, K]]
[[Category: Scheerer, P]]
[[Category: Lamparter, T]]
[[Category: Nagano, S]]