6mhi - Revision history

OCA at 06:32, 11 October 2023

OCA — Wed, 11 Oct 2023 06:32:01 GMT

←Older revision		Revision as of 06:32, 11 October 2023
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	<StructureSection load='6mhi' size='340' side='right'caption='[[6mhi]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6mhi' size='340' side='right'caption='[[6mhi]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mhi]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_244 Dsm 244~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MHI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MHI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mhi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MHI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MHI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=YYZ:(2E)~~-~~3-(3~~,~~5-dichloro-4-hydroxyphenyl)prop-2-enoic+acid'>YYZ</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]] 1.35Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=1053 DSM 244]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YYZ:(2E)-3-(3,5-dichloro-4-hydroxyphenyl)prop-2-enoic+acid'>YYZ</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=6mhi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mhi OCA], [~~http~~://pdbe.org/6mhi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mhi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mhi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mhi 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=6mhi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mhi OCA], [https://pdbe.org/6mhi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mhi RCSB], [https://www.ebi.ac.uk/pdbsum/6mhi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mhi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.	+	[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
	<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: ~~Dsm 244~~]]	+	[[Category: Halorhodospira halophila]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Both, J]]	+	[[Category: Both J]]
-	[[Category: Boxer~~, S G~~]]	+	[[Category: Boxer SG]]
-	[[Category: Martinez, T]]	+	[[Category: Martinez T]]
-	[[Category: Parrish~~, R M~~]]	+	[[Category: Parrish RM]]
-	[[Category: Thomson~~, B D~~]]	+	[[Category: Thomson BD]]
-	[[Category: Wu, Y]]	+	[[Category: Wu Y]]
-	~~[[Category: Active site]]~~	+
-	~~[[Category: Chlorinated chromophore]]~~	+
-	~~[[Category: Hydrogen bonding network]]~~	+
-	~~[[Category: Low-barrier hydrogen bond]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 23:06, 5 June 2019

OCA — Wed, 05 Jun 2019 23:06:44 GMT

←Older revision		Revision as of 23:06, 5 June 2019
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	<StructureSection load='6mhi' size='340' side='right'caption='[[6mhi]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6mhi' size='340' side='right'caption='[[6mhi]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mhi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MHI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MHI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mhi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MHI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MHI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YYZ:(2E)-3-(3,5-dichloro-4-hydroxyphenyl)prop-2-enoic+acid'>YYZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YYZ:(2E)-3-(3,5-dichloro-4-hydroxyphenyl)prop-2-enoic+acid'>YYZ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=6mhi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mhi OCA], [http://pdbe.org/6mhi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mhi RCSB], [http://www.ebi.ac.uk/pdbsum/6mhi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mhi 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=6mhi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mhi OCA], [http://pdbe.org/6mhi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mhi RCSB], [http://www.ebi.ac.uk/pdbsum/6mhi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mhi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.		[[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.
		+
		+	Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.,Thomson B, Both J, Wu Y, Parrish RM, Martinez TJ, Boxer SG J Phys Chem B. 2019 May 31. doi: 10.1021/acs.jpcb.9b01571. PMID:31117606<ref>PMID:31117606</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mhi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dsm 244]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Both, J]]		[[Category: Both, J]]

OCA at 06:13, 29 May 2019

OCA — Wed, 29 May 2019 06:13:19 GMT

←Older revision		Revision as of 06:13, 29 May 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6mhi ~~is ON HOLD until Paper Publication~~	+	==Photoactive Yellow Protein with covalently bound 3,5-dichloro-4-hydroxycinnamic acid chromophore==
-		+	<StructureSection load='6mhi' size='340' side='right'caption='[[6mhi]], [[Resolution\|resolution]] 1.35Å' scene=''>
-	~~Authors~~: ~~Thomson, B~~.D.~~, Both, J~~.~~, Wu, Y~~.~~, Parrish, R~~.M.~~, Martinez, T~~.~~, Boxer, S~~.G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mhi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MHI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MHI FirstGlance]. <br>
-	~~Description~~: ~~Photoactive Yellow Protein with covalently bound~~ 3,5-dichloro-4-~~hydroxycinnamic~~ acid ~~chromophore~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YYZ:(2E)-3-(3,5-dichloro-4-hydroxyphenyl)prop-2-enoic+acid'>YYZ</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=6mhi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mhi OCA], [http://pdbe.org/6mhi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mhi RCSB], [http://www.ebi.ac.uk/pdbsum/6mhi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mhi ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Both, J]]		[[Category: Both, J]]
-	[[Category: Parrish, R.M]]	+	[[Category: Boxer, S G]]
		+	[[Category: Martinez, T]]
		+	[[Category: Parrish, R M]]
		+	[[Category: Thomson, B D]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
-	[[Category: ~~Martinez, T~~]]	+	[[Category: Active site]]
-	[[Category: ~~Boxer, S.G~~]]	+	[[Category: Chlorinated chromophore]]
-	[[Category: ~~Thomson, B.D~~]]	+	[[Category: Hydrogen bonding network]]
		+	[[Category: Low-barrier hydrogen bond]]
		+	[[Category: Signaling protein]]

OCA at 06:25, 3 October 2018

OCA — Wed, 03 Oct 2018 06:25:13 GMT

←Older revision		Revision as of 06:25, 3 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Thomson, B.D., Both, J., Wu, Y., Parrish, R.M., Martinez, T., Boxer, S.G.		Authors: Thomson, B.D., Both, J., Wu, Y., Parrish, R.M., Martinez, T., Boxer, S.G.
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	Description: Photoactive Yellow Protein with covalently bound 3,5-dichloro-4-hydroxycinnamic acid chromophore		Description: Photoactive Yellow Protein with covalently bound 3,5-dichloro-4-hydroxycinnamic acid chromophore
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Parrish, R.M]]
-	[[Category: Boxer, S.G]]
	[[Category: Both, J]]		[[Category: Both, J]]
		+	[[Category: Parrish, R.M]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
	[[Category: Martinez, T]]		[[Category: Martinez, T]]
		+	[[Category: Boxer, S.G]]
	[[Category: Thomson, B.D]]		[[Category: Thomson, B.D]]

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

OCA — Wed, 26 Sep 2018 06:33:08 GMT

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

←Older revision

Revision as of 06:33, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6mhi is ON HOLD Authors: Thomson, B.D., Both, J., Wu, Y., Parrish, R.M., Martinez, T., Boxer, S.G. Description: Photoactive Yellow Protein with cov...

OCA — Wed, 26 Sep 2018 06:33:06 GMT

New page: '''Unreleased structure''' The entry 6mhi is ON HOLD Authors: Thomson, B.D., Both, J., Wu, Y., Parrish, R.M., Martinez, T., Boxer, S.G. Description: Photoactive Yellow Protein with cov...

New page

'''Unreleased structure'''

The entry 6mhi is ON HOLD

Authors: Thomson, B.D., Both, J., Wu, Y., Parrish, R.M., Martinez, T., Boxer, S.G.

Description: Photoactive Yellow Protein with covalently bound 3,5-dichloro-4-hydroxycinnamic acid chromophore
[[Category: Unreleased Structures]]
[[Category: Parrish, R.M]]
[[Category: Boxer, S.G]]
[[Category: Both, J]]
[[Category: Wu, Y]]
[[Category: Martinez, T]]
[[Category: Thomson, B.D]]