7ltd - Revision history

OCA at 15:58, 18 October 2023

2023-10-18T15:58:51Z

←Older revision		Revision as of 15:58, 18 October 2023
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	==X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1==		==X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1==
-	<StructureSection load='7ltd' size='340' side='right'caption='[[7ltd]]' scene=''>	+	<StructureSection load='7ltd' size='340' side='right'caption='[[7ltd]], [[Resolution\|resolution]] 0.90Å' 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=7LTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LTD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ltd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Parengyodontium_album Parengyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LTD 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=7ltd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ltd OCA], [https://pdbe.org/7ltd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ltd RCSB], [https://www.ebi.ac.uk/pdbsum/7ltd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ltd 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]] 0.9Å</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=NO3:NITRATE+ION'>NO3</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=7ltd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ltd OCA], [https://pdbe.org/7ltd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ltd RCSB], [https://www.ebi.ac.uk/pdbsum/7ltd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ltd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PRTK_PARAQ PRTK_PARAQ] Hydrolyzes keratin at aromatic and hydrophobic residues.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cryo-cooling has been nearly universally adopted to mitigate X-ray damage and facilitate crystal handling in protein X-ray crystallography. However, cryo X-ray crystallographic data provide an incomplete window into the ensemble of conformations that is at the heart of protein function and energetics. Room-temperature (RT) X-ray crystallography provides accurate ensemble information, and recent developments allow conformational heterogeneity (the experimental manifestation of ensembles) to be extracted from single-crystal data. Nevertheless, high sensitivity to X-ray damage at RT raises concerns about data reliability. To systematically address this critical issue, increasingly X-ray-damaged high-resolution data sets (1.02-1.52 A resolution) were obtained from single proteinase K, thaumatin and lysozyme crystals at RT (277 K). In each case a modest increase in conformational heterogeneity with X-ray damage was observed. Merging data with different extents of damage (as is typically carried out) had negligible effects on conformational heterogeneity until the overall diffraction intensity decayed to approximately 70% of its initial value. These effects were compared with X-ray damage effects in cryo-cooled crystals by carrying out an analogous analysis of increasingly damaged proteinase K cryo data sets (0.9-1.16 A resolution). X-ray damage-associated heterogeneity changes were found that were not observed at RT. This property renders it difficult to distinguish real from artefactual conformations and to determine the conformational response to changes in temperature. The ability to acquire reliable heterogeneity information from single crystals at RT, together with recent advances in RT data collection at accessible synchrotron beamlines, provides a strong motivation for the widespread adoption of RT X-ray crystallography to obtain conformational ensemble information.
		+
		+	Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.,Yabukarski F, Doukov T, Mokhtari DA, Du S, Herschlag D Acta Crystallogr D Struct Biol. 2022 Aug 1;78(Pt 8):945-963. doi:, 10.1107/S2059798322005939. Epub 2022 Jul 14. PMID:35916220<ref>PMID:35916220</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ltd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proteinase 3D structures\|Proteinase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Parengyodontium album]]
	[[Category: Doukov T]]		[[Category: Doukov T]]
	[[Category: Herschlag D]]		[[Category: Herschlag D]]
	[[Category: Yabukarski F]]		[[Category: Yabukarski F]]

OCA at 06:15, 18 August 2022

2022-08-18T06:15:06Z

←Older revision		Revision as of 06:15, 18 August 2022
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-	'''Unreleased structure'''

-	~~The entry 7ltd is ON HOLD until Paper Publication~~	+	==X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1==
-		+	<StructureSection load='7ltd' size='340' side='right'caption='[[7ltd]]' scene=''>
-	~~Authors: Yabukarski, F., Doukov, T., Herschlag, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LTD FirstGlance]. <br>
-	~~Description:~~ X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1	+	</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=7ltd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ltd OCA], [https://pdbe.org/7ltd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ltd RCSB], [https://www.ebi.ac.uk/pdbsum/7ltd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ltd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Doukov, T]]	+	__TOC__
-	[[Category: Herschlag, D]]	+	</StructureSection>
-	[[Category: Yabukarski, F]]	+	[[Category: Large Structures]]
		+	[[Category: Doukov T]]
		+	[[Category: Herschlag D]]
		+	[[Category: Yabukarski F]]

OCA at 05:29, 24 March 2021

2021-03-24T05:29:41Z

←Older revision		Revision as of 05:29, 24 March 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yabukarski, F., Doukov, T., Herschlag, D.		Authors: Yabukarski, F., Doukov, T., Herschlag, D.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Doukov, T]]		[[Category: Doukov, T]]
-	[[Category: Yabukarski, F]]
	[[Category: Herschlag, D]]		[[Category: Herschlag, D]]
		+	[[Category: Yabukarski, F]]

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

2021-03-03T13:24:21Z

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

←Older revision

Revision as of 13:24, 3 March 2021

OCA: New page: '''Unreleased structure''' The entry 7ltd is ON HOLD Authors: Yabukarski, F., Doukov, T., Herschlag, D. Description: X-ray radiation damage series on Proteinase K at 100K, crystal stru...

2021-03-03T13:24:20Z

New page: '''Unreleased structure''' The entry 7ltd is ON HOLD Authors: Yabukarski, F., Doukov, T., Herschlag, D. Description: X-ray radiation damage series on Proteinase K at 100K, crystal stru...

New page

'''Unreleased structure'''

The entry 7ltd is ON HOLD

Authors: Yabukarski, F., Doukov, T., Herschlag, D.

Description: X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1
[[Category: Unreleased Structures]]
[[Category: Doukov, T]]
[[Category: Yabukarski, F]]
[[Category: Herschlag, D]]