6q88 - Revision history

OCA at 11:55, 24 January 2024

OCA — Wed, 24 Jan 2024 11:55:11 GMT

←Older revision		Revision as of 11:55, 24 January 2024
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	<StructureSection load='6q88' size='340' side='right'caption='[[6q88]], [[Resolution\|resolution]] 1.74Å' scene=''>		<StructureSection load='6q88' size='340' side='right'caption='[[6q88]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q88]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q88 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6Q88 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q88 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.7400706Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Lysozyme Lysozyme]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6q88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q88 OCA], [~~http~~://pdbe.org/6q88 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6q88 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6q88 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6q88 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=6q88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q88 OCA], [https://pdbe.org/6q88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q88 RCSB], [https://www.ebi.ac.uk/pdbsum/6q88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q88 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>	+	[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6q88" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6q88" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Burghammer M]]
-	[[Category: Burghammer, M]]	+	[[Category: Bury CS]]
-	[[Category: Bury~~, C S~~]]	+	[[Category: Colletier JP]]
-	[[Category: Colletier~~, J P~~]]	+	[[Category: Coquelle N]]
-	[[Category: Coquelle, N]]	+	[[Category: Garman EF]]
-	[[Category: Garman~~, E F]]~~	+	[[Category: Rosenthal M]]
-	~~[[Category: Mora, E de la~~]]	+	[[Category: Weik M]]
-	[[Category: Rosenthal, M]]	+	[[Category: De la Mora E]]
-	[[Category: Weik, M]]	+
-	[[Category: ~~Antimicrobial]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Low-dose]]~~	+
-	~~[[Category: Serial crystallography~~]]	+

OCA at 10:27, 26 February 2020

OCA — Wed, 26 Feb 2020 10:27:46 GMT

←Older revision		Revision as of 10:27, 26 February 2020
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>		[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-A resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses (D 1/2) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 A.
		+
		+	Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures.,de la Mora E, Coquelle N, Bury CS, Rosenthal M, Holton JM, Carmichael I, Garman EF, Burghammer M, Colletier JP, Weik M Proc Natl Acad Sci U S A. 2020 Feb 11. pii: 1821522117. doi:, 10.1073/pnas.1821522117. PMID:32047034<ref>PMID:32047034</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6q88" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:47, 22 January 2020

OCA — Wed, 22 Jan 2020 16:47:07 GMT

←Older revision		Revision as of 16:47, 22 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6q88 ~~is ON HOLD~~	+	==RT structure of HEWL at 5 kGy==
-		+	<StructureSection load='6q88' size='340' side='right'caption='[[6q88]], [[Resolution\|resolution]] 1.74Å' scene=''>
-	~~Authors~~: ~~de la Mora, E~~.~~, Coquelle, N~~.~~, Bury, C~~.S., ~~Rosenthal~~, M., ~~Garman, E~~.F., ~~Burghammer~~, M., ~~Colletier, J~~.P., ~~Weik,~~ M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6q88]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q88 FirstGlance]. <br>
-	~~Description~~: ~~HEWL structure at 4 kGy~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
-	[[Category: ~~Garman~~, ~~E.F~~]]	+	<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=6q88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q88 OCA], [http://pdbe.org/6q88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q88 RCSB], [http://www.ebi.ac.uk/pdbsum/6q88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q88 ProSAT]</span></td></tr>
-	[[Category: Bury, C.S]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
		+	[[Category: Lysozyme]]
		+	[[Category: Burghammer, M]]
		+	[[Category: Bury, C S]]
		+	[[Category: Colletier, J P]]
	[[Category: Coquelle, N]]		[[Category: Coquelle, N]]
-	[[Category: ~~Colletier~~, ~~J.P~~]]	+	[[Category: Garman, E F]]
		+	[[Category: Mora, E de la]]
	[[Category: Rosenthal, M]]		[[Category: Rosenthal, M]]
-	[[Category: De La Mora, E]]
-	[[Category: Burghammer, M]]
	[[Category: Weik, M]]		[[Category: Weik, M]]
		+	[[Category: Antimicrobial]]
		+	[[Category: Hydrolase]]
		+	[[Category: Low-dose]]
		+	[[Category: Serial crystallography]]

OCA: Protected "6q88" [edit=sysop:move=sysop]

OCA — Wed, 26 Dec 2018 06:55:59 GMT

Protected "6q88" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:55, 26 December 2018

OCA: New page: '''Unreleased structure''' The entry 6q88 is ON HOLD Authors: de la Mora, E., Coquelle, N., Bury, C.S., Rosenthal, M., Garman, E.F., Burghammer, M., Colletier, J.P., Weik, M. Descripti...

OCA — Wed, 26 Dec 2018 06:55:57 GMT

New page: '''Unreleased structure''' The entry 6q88 is ON HOLD Authors: de la Mora, E., Coquelle, N., Bury, C.S., Rosenthal, M., Garman, E.F., Burghammer, M., Colletier, J.P., Weik, M. Descripti...

New page

'''Unreleased structure'''

The entry 6q88 is ON HOLD

Authors: de la Mora, E., Coquelle, N., Bury, C.S., Rosenthal, M., Garman, E.F., Burghammer, M., Colletier, J.P., Weik, M.

Description: HEWL structure at 4 kGy
[[Category: Unreleased Structures]]
[[Category: Garman, E.F]]
[[Category: Bury, C.S]]
[[Category: Coquelle, N]]
[[Category: Colletier, J.P]]
[[Category: Rosenthal, M]]
[[Category: De La Mora, E]]
[[Category: Burghammer, M]]
[[Category: Weik, M]]