6svw - Revision history

OCA at 16:21, 29 January 2020

OCA — Wed, 29 Jan 2020 16:21:48 GMT

←Older revision		Revision as of 16:21, 29 January 2020
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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=6svw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6svw OCA], [http://pdbe.org/6svw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6svw RCSB], [http://www.ebi.ac.uk/pdbsum/6svw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6svw 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=6svw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6svw OCA], [http://pdbe.org/6svw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6svw RCSB], [http://www.ebi.ac.uk/pdbsum/6svw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6svw ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.
		+
		+	Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.,Gagner VA, Lundholm I, Garcia-Bonete MJ, Rodilla H, Friedman R, Zhaunerchyk V, Bourenkov G, Schneider T, Stake J, Katona G Sci Rep. 2019 Dec 17;9(1):19281. doi: 10.1038/s41598-019-55777-5. PMID:31848402<ref>PMID:31848402</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6svw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:19, 22 January 2020

OCA — Wed, 22 Jan 2020 16:19:04 GMT

←Older revision		Revision as of 16:19, 22 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6svw ~~is ON HOLD until Paper Publication~~	+	==Reference structure of bovine trypsin (even frames of crystal x33)==
-		+	<StructureSection load='6svw' size='340' side='right'caption='[[6svw]], [[Resolution\|resolution]] 1.16Å' scene=''>
-	~~Authors~~: ~~Ahlberg Gagner, V~~., ~~Lundholm~~, I., ~~Garcia~~-~~Bonete~~, M.J., ~~Rodilla, H~~., ~~Friedman, R~~., ~~Zhaunerchyk, V~~., Bourenkov, G., ~~Schneider~~, ~~T., Stake~~, J., Katona, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6svw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SVW FirstGlance]. <br>
-	~~Description: Reference structure of bovine trypsin (even frames of crystal x33)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=6svw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6svw OCA], [http://pdbe.org/6svw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6svw RCSB], [http://www.ebi.ac.uk/pdbsum/6svw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6svw ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Large Structures]]
		+	[[Category: Trypsin]]
		+	[[Category: Bourenkov, G]]
		+	[[Category: Friedman, R]]
		+	[[Category: Gagner, V Ahlberg]]
		+	[[Category: Garcia-Bonete, M J]]
		+	[[Category: Katona, G]]
		+	[[Category: Lundholm, I]]
	[[Category: Rodilla, H]]		[[Category: Rodilla, H]]
		+	[[Category: Schneider, T]]
	[[Category: Stake, J]]		[[Category: Stake, J]]
-	[[Category: Schneider, T]]
	[[Category: Zhaunerchyk, V]]		[[Category: Zhaunerchyk, V]]
-	[[Category: ~~Garcia-Bonete, M.J~~]]	+	[[Category: Bovine trypsin]]
-	[[Category: ~~Lundholm, I~~]]	+	[[Category: Even frame]]
-	[[Category: ~~Bourenkov, G~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~Ahlberg Gagner, V~~]]	+	[[Category: Terahertz irradiation]]
-	[[Category: ~~Katona, G]]~~	+	[[Category: X33]]
-	~~[[Category: Friedman, R~~]]	+

OCA at 09:23, 13 November 2019

OCA — Wed, 13 Nov 2019 09:23:15 GMT

←Older revision		Revision as of 09:23, 13 November 2019
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	The entry 6svw is ON HOLD until Paper Publication		The entry 6svw is ON HOLD until Paper Publication

-	Authors:	+	Authors: Ahlberg Gagner, V., Lundholm, I., Garcia-Bonete, M.J., Rodilla, H., Friedman, R., Zhaunerchyk, V., Bourenkov, G., Schneider, T., Stake, J., Katona, G.

-	Description:	+	Description: Reference structure of bovine trypsin (even frames of crystal x33)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Rodilla, H]]
		+	[[Category: Stake, J]]
		+	[[Category: Schneider, T]]
		+	[[Category: Zhaunerchyk, V]]
		+	[[Category: Garcia-Bonete, M.J]]
		+	[[Category: Lundholm, I]]
		+	[[Category: Bourenkov, G]]
		+	[[Category: Ahlberg Gagner, V]]
		+	[[Category: Katona, G]]
		+	[[Category: Friedman, R]]

OCA at 04:24, 16 October 2019

OCA — Wed, 16 Oct 2019 04:24:00 GMT

←Older revision		Revision as of 04:24, 16 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 02 Oct 2019 07:54:01 GMT

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

←Older revision

Revision as of 07:54, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6svw is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Oct 2019 07:53:59 GMT

New page: '''Unreleased structure''' The entry 6svw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6svw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]