8dct - Revision history

OCA at 17:27, 18 October 2023

OCA — Wed, 18 Oct 2023 17:27:01 GMT

←Older revision		Revision as of 17:27, 18 October 2023
Line 1:		Line 1:

	==Lysozyme cluster 3 dual apo structure==		==Lysozyme cluster 3 dual apo structure==
-	<StructureSection load='8dct' size='340' side='right'caption='[[8dct]]' scene=''>	+	<StructureSection load='8dct' size='340' side='right'caption='[[8dct]], [[Resolution\|resolution]] 2.00Å' 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=8DCT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8dct]] 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=8DCT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCT 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=8dct FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dct OCA], [https://pdbe.org/8dct PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dct RCSB], [https://www.ebi.ac.uk/pdbsum/8dct PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dct 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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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=8dct FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dct OCA], [https://pdbe.org/8dct PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dct RCSB], [https://www.ebi.ac.uk/pdbsum/8dct PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dct ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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;">
		+	== Publication Abstract from PubMed ==
		+	KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.
		+
		+	Serial crystallography with multi-stage merging of thousands of images.,Soares AS, Yamada Y, Jakoncic J, McSweeney S, Sweet RM, Skinner J, Foadi J, Fuchs MR, Schneider DK, Shi W, Andi B, Andrews LC, Bernstein HJ Acta Crystallogr F Struct Biol Commun. 2022 Jul 1;78(Pt 7):281-288. doi:, 10.1107/S2053230X22006422. Epub 2022 Jul 4. PMID:35787556<ref>PMID:35787556</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8dct" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bernstein HJ]]		[[Category: Bernstein HJ]]

OCA at 06:25, 18 August 2022

OCA — Thu, 18 Aug 2022 06:25:36 GMT

←Older revision		Revision as of 06:25, 18 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 8dct ~~is ON HOLD~~	+	==Lysozyme cluster 3 dual apo structure==
-		+	<StructureSection load='8dct' size='340' side='right'caption='[[8dct]]' scene=''>
-	~~Authors~~: ~~Soares, A~~.S., ~~Yamada~~, Y., ~~Jakoncic, J~~., ~~Schneider, D~~.K., ~~Bernstein, H~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCT FirstGlance]. <br>
-	~~Description: Lysozyme cluster 3 dual apo structure~~	+	</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=8dct FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dct OCA], [https://pdbe.org/8dct PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dct RCSB], [https://www.ebi.ac.uk/pdbsum/8dct PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dct ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Soares, A.S~~]]	+	__TOC__
-	[[Category: ~~Bernstein, H.~~J]]	+	</StructureSection>
-	[[Category: Schneider~~, D.K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Jakoncic, J~~]]	+	[[Category: Bernstein HJ]]
-	[[Category: Yamada, Y]]	+	[[Category: Jakoncic J]]
		+	[[Category: Schneider DK]]
		+	[[Category: Soares AS]]
		+	[[Category: Yamada Y]]

OCA at 15:11, 6 July 2022

OCA — Wed, 06 Jul 2022 15:11:32 GMT

←Older revision		Revision as of 15:11, 6 July 2022
Line 5:		Line 5:
	Authors: Soares, A.S., Yamada, Y., Jakoncic, J., Schneider, D.K., Bernstein, H.J.		Authors: Soares, A.S., Yamada, Y., Jakoncic, J., Schneider, D.K., Bernstein, H.J.

-	Description: ~~Serial Crystallography with Multi-stage Merging of 1000s of Images~~	+	Description: Lysozyme cluster 3 dual apo structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Soares, A.S]]
	[[Category: Bernstein, H.J]]		[[Category: Bernstein, H.J]]
	[[Category: Schneider, D.K]]		[[Category: Schneider, D.K]]
-	[[Category: Soares, A.S]]
	[[Category: Jakoncic, J]]		[[Category: Jakoncic, J]]
	[[Category: Yamada, Y]]		[[Category: Yamada, Y]]

OCA: Protected "8dct" [edit=sysop:move=sysop]

OCA — Wed, 29 Jun 2022 06:28:20 GMT

Protected "8dct" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:28, 29 June 2022

OCA: New page: '''Unreleased structure''' The entry 8dct is ON HOLD Authors: Soares, A.S., Yamada, Y., Jakoncic, J., Schneider, D.K., Bernstein, H.J. Description: Serial Crystallography with Multi-st...

OCA — Wed, 29 Jun 2022 06:28:19 GMT

New page: '''Unreleased structure''' The entry 8dct is ON HOLD Authors: Soares, A.S., Yamada, Y., Jakoncic, J., Schneider, D.K., Bernstein, H.J. Description: Serial Crystallography with Multi-st...

New page

'''Unreleased structure'''

The entry 8dct is ON HOLD

Authors: Soares, A.S., Yamada, Y., Jakoncic, J., Schneider, D.K., Bernstein, H.J.

Description: Serial Crystallography with Multi-stage Merging of 1000s of Images
[[Category: Unreleased Structures]]
[[Category: Bernstein, H.J]]
[[Category: Schneider, D.K]]
[[Category: Soares, A.S]]
[[Category: Jakoncic, J]]
[[Category: Yamada, Y]]