7spx - Revision history

OCA at 16:54, 18 October 2023

2023-10-18T16:54:06Z

←Older revision		Revision as of 16:54, 18 October 2023
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	==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==		==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==
-	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]]' scene=''>	+	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]], [[Resolution\|resolution]] 0.97Å' 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=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7spx]] 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=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX 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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx ProSAT]</span></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]] 0.97Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9IJ:2-cyano-L-phenylalanine'>9IJ</scene>, <scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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;">
		+	== Publication Abstract from PubMed ==
		+	Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C identical withN bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.
		+
		+	Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments.,Weaver JB, Kozuch J, Kirsh JM, Boxer SG J Am Chem Soc. 2022 May 4;144(17):7562-7567. doi: 10.1021/jacs.2c00675. Epub 2022, Apr 25. PMID:35467853<ref>PMID:35467853</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7spx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Halorhodospira halophila]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Boxer SG]]		[[Category: Boxer SG]]
	[[Category: Kirsh JM]]		[[Category: Kirsh JM]]
-	[[Category: Weaver JW]]	+	[[Category: Weaver JB]]

OCA at 14:36, 31 August 2022

2022-08-31T14:36:48Z

←Older revision		Revision as of 14:36, 31 August 2022
Line 1:		Line 1:

	==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==		==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==
-	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]]~~, [[Resolution\|resolution]] 0.97Å~~' scene=''>	+	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7spx]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>~~	+	</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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx ProSAT]</span></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9IJ:'>9IJ</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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[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;">
-	== Publication Abstract from PubMed ==
-	Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C identical withN bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.
-
-	Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments.,Weaver JB, Kozuch J, Kirsh JM, Boxer SG J Am Chem Soc. 2022 May 4;144(17):7562-7567. doi: 10.1021/jacs.2c00675. Epub 2022, Apr 25. PMID:35467853<ref>PMID:35467853</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7spx" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boxer~~, S G~~]]	+	[[Category: Boxer SG]]
-	[[Category: Kirsh~~, J M~~]]	+	[[Category: Kirsh JM]]
-	[[Category: Weaver~~, J B]]~~	+	[[Category: Weaver JW]]
-	~~[[Category: Photoreceptor]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 06:40, 18 August 2022

2022-08-18T06:40:24Z

←Older revision		Revision as of 06:40, 18 August 2022
Line 26:		Line 26:
	[[Category: Boxer, S G]]		[[Category: Boxer, S G]]
	[[Category: Kirsh, J M]]		[[Category: Kirsh, J M]]
-	[[Category: Weaver, J W]]	+	[[Category: Weaver, J B]]
	[[Category: Photoreceptor]]		[[Category: Photoreceptor]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA at 10:26, 18 May 2022

2022-05-18T10:26:16Z

←Older revision		Revision as of 10:26, 18 May 2022
Line 1:		Line 1:

	==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==		==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==
-	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]]' scene=''>	+	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]], [[Resolution\|resolution]] 0.97Å' 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=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7spx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX 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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx 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=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9IJ:'>9IJ</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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[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;">
		+	== Publication Abstract from PubMed ==
		+	Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C identical withN bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.
		+
		+	Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments.,Weaver JB, Kozuch J, Kirsh JM, Boxer SG J Am Chem Soc. 2022 May 4;144(17):7562-7567. doi: 10.1021/jacs.2c00675. Epub 2022, Apr 25. PMID:35467853<ref>PMID:35467853</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7spx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boxer SG]]	+	[[Category: Boxer, S G]]
-	[[Category: Kirsh JM]]	+	[[Category: Kirsh, J M]]
-	[[Category: Weaver JW]]	+	[[Category: Weaver, J W]]
		+	[[Category: Photoreceptor]]
		+	[[Category: Signaling protein]]

OCA at 06:20, 12 May 2022

2022-05-12T06:20:19Z

←Older revision		Revision as of 06:20, 12 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7spx is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of photoactive yellow protein (PYP); F28oCNF construct==
-		+	<StructureSection load='7spx' size='340' side='right'caption='[[7spx]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SPX 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=7spx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7spx OCA], [https://pdbe.org/7spx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7spx RCSB], [https://www.ebi.ac.uk/pdbsum/7spx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7spx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Boxer SG]]
		+	[[Category: Kirsh JM]]
		+	[[Category: Weaver JW]]

OCA at 08:33, 8 December 2021

2021-12-08T08:33:40Z

←Older revision		Revision as of 08:33, 8 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2021-11-10T05:19:06Z

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

←Older revision

Revision as of 05:19, 10 November 2021

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

2021-11-10T05:19:05Z

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

New page

'''Unreleased structure'''

The entry 7spx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]