6sim - Revision history

OCA at 08:19, 17 October 2024

2024-10-17T08:19:46Z

← Older revision		Revision as of 08:19, 17 October 2024
Line 3:		Line 3:
	<StructureSection load='6sim' size='340' side='right'caption='[[6sim]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='6sim' size='340' side='right'caption='[[6sim]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6sim]] 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=6SIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[6sim]] 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=6SIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.6101803Å</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6sim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sim OCA], [~~http~~://pdbe.org/6sim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6sim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6sim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6sim 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=6sim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sim OCA], [https://pdbe.org/6sim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sim RCSB], [https://www.ebi.ac.uk/pdbsum/6sim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sim 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 ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6sim" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6sim" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Lysozyme]]~~		[[Category: Garcia-Bonete MJ]]
	[[Category: Garcia-Bonete~~, M J~~]]		[[Category: Katona G]]
	[[Category: Katona, G]]
	~~[[Category: Hen egg white lysozyme]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Inverse beam geometry collection]]~~
	~~[[Category: Single-wavelength x-ray anomalous diffraction]]~~
	~~[[Category: Univariate analysis~~]]

OCA at 11:51, 13 November 2019

2019-11-13T11:51:23Z

← Older revision		Revision as of 11:51, 13 November 2019
Line 10:		Line 10:
	== 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 ==
			Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.

			Bayesian machine learning improves single-wavelength anomalous diffraction phasing.,Garcia-Bonete MJ, Katona G Acta Crystallogr A Found Adv. 2019 Nov 1;75(Pt 6):851-860. doi:, 10.1107/S2053273319011446. Epub 2019 Oct 7. PMID:31692460<ref>PMID:31692460</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6sim" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:51, 6 November 2019

2019-11-06T06:51:15Z

← Older revision		Revision as of 06:51, 6 November 2019
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry 6sim is ON HOLD until Paper Publication~~		==SAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry data collection and univariate analysis==
			<StructureSection load='6sim' size='340' side='right'caption='[[6sim]], [[Resolution\|resolution]] 1.61Å' scene=''>
	~~Authors: Garcia-Bonete, M.J., Katona, G.~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[6sim]] 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=6SIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SIM FirstGlance]. <br>
	~~Description:~~ SAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry data collection and univariate analysis		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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>
			<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=6sim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sim OCA], [http://pdbe.org/6sim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sim RCSB], [http://www.ebi.ac.uk/pdbsum/6sim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sim ProSAT]</span></td></tr>
			</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: Garcia-Bonete, M J]]
	[[Category: Katona, G]]		[[Category: Katona, G]]
	[[Category: ~~Garcia~~-~~Bonete, M.J~~]]		[[Category: Hen egg white lysozyme]]
			[[Category: Hydrolase]]
			[[Category: Inverse beam geometry collection]]
			[[Category: Single-wavelength x-ray anomalous diffraction]]
			[[Category: Univariate analysis]]

OCA at 04:22, 16 October 2019

2019-10-16T04:22:47Z

← Older revision		Revision as of 04:22, 16 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6sim is ON HOLD		The entry 6sim is ON HOLD until Paper Publication

	Authors: Garcia-Bonete, M.J., Katona, G.		Authors: Garcia-Bonete, M.J., Katona, G.

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

2019-08-21T04:17:26Z

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

← Older revision	Revision as of 04:17, 21 August 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6sim is ON HOLD Authors: Garcia-Bonete, M.J., Katona, G. Description: SAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry da...

2019-08-21T04:17:24Z

New page: '''Unreleased structure''' The entry 6sim is ON HOLD Authors: Garcia-Bonete, M.J., Katona, G. Description: SAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry da...

New page

'''Unreleased structure'''

The entry 6sim is ON HOLD

Authors: Garcia-Bonete, M.J., Katona, G.

Description: SAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry data collection and univariate analysis
[[Category: Unreleased Structures]]
[[Category: Katona, G]]
[[Category: Garcia-Bonete, M.J]]