6myv - Revision history

OCA at 06:42, 11 October 2023

OCA — Wed, 11 Oct 2023 06:42:06 GMT

←Older revision		Revision as of 06:42, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6myv' size='340' side='right'caption='[[6myv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6myv' size='340' side='right'caption='[[6myv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6myv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6MYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6myv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacterium Bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GC9:2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic+acid'>GC9</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]] 2.2Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6myv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myv OCA], [~~http~~://pdbe.org/6myv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6myv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6myv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6myv ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GC9:2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic+acid'>GC9</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=6myv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myv OCA], [https://pdbe.org/6myv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6myv RCSB], [https://www.ebi.ac.uk/pdbsum/6myv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6myv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A4S2B4D9_9BACE A0A4S2B4D9_9BACE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6myv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6myv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Neuraminidase 3D structures\|Neuraminidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Alisson-Silva, F]]	+	[[Category: Alisson-Silva F]]
-	[[Category: Chang, G]]	+	[[Category: Chang G]]
-	[[Category: Chuzel, L]]	+	[[Category: Chuzel L]]
-	[[Category: Diaz~~, S L~~]]	+	[[Category: Diaz SL]]
-	[[Category: Ganatra~~, M B~~]]	+	[[Category: Ganatra MB]]
-	[[Category: Huang, J]]	+	[[Category: Huang J]]
-	[[Category: Martino, C]]	+	[[Category: Martino C]]
-	[[Category: Rees~~, S D~~]]	+	[[Category: Rees SD]]
-	[[Category: Siegel, D]]	+	[[Category: Siegel D]]
-	[[Category: Taron~~, C H~~]]	+	[[Category: Taron CH]]
-	[[Category: Varki, A]]	+	[[Category: Varki A]]
-	[[Category: Zaramela~~, L S~~]]	+	[[Category: Zaramela LS]]
-	[[Category: Zengler, K]]	+	[[Category: Zengler K]]
-	[[Category: Zuniga, C]]	+	[[Category: Zuniga C]]
-	~~[[Category: Dana]]~~	+
-	~~[[Category: Dana-gc]]~~	+
-	~~[[Category: Gc]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inflammation]]~~	+
-	~~[[Category: Microbiome]]~~	+
-	~~[[Category: Neu5gc]]~~	+
-	~~[[Category: Neu5gc2en]]~~	+
-	~~[[Category: Sialic acid]]~~	+
-	~~[[Category: Sialidase~~]]	+

OCA at 06:02, 22 April 2020

OCA — Wed, 22 Apr 2020 06:02:21 GMT

←Older revision		Revision as of 06:02, 22 April 2020
Line 3:		Line 3:
	<StructureSection load='6myv' size='340' side='right'caption='[[6myv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6myv' size='340' side='right'caption='[[6myv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6myv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6myv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6MYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GC9:2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic+acid'>GC9</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GC9:2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic+acid'>GC9</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=6myv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myv OCA], [http://pdbe.org/6myv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myv RCSB], [http://www.ebi.ac.uk/pdbsum/6myv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myv ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6myv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myv OCA], [http://pdbe.org/6myv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myv RCSB], [http://www.ebi.ac.uk/pdbsum/6myv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:11, 10 October 2019

OCA — Thu, 10 Oct 2019 06:11:38 GMT

←Older revision		Revision as of 06:11, 10 October 2019
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~phenix~~.~~refine~~ is a ~~program within the PHENIX package that supports crystallographic structure refinement against experimental data~~ with ~~a wide range~~ of ~~upper resolution limits using a large repertoire of model parameterizations~~. ~~It has several automation features and~~ is ~~also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user~~-~~defined refinement strategies can~~ be ~~applied to specific parts of the model~~ in a ~~single refinement run~~. ~~An intuitive graphical user interface~~ is ~~available~~ to ~~guide novice users and to assist advanced users in managing refinement projects~~. X-~~ray or neutron diffraction data can be used separately or jointly~~ in ~~refinement. phenix.refine is tightly integrated into~~ the ~~PHENIX suite~~, ~~where it serves as a critical component in automated model building, final structure refinement, structure validation~~ and ~~deposition to~~ the ~~wwPDB~~. ~~This paper presents an overview~~ of ~~the major phenix.refine features,~~ with ~~extensive literature references~~ for ~~readers interested in more detailed discussions~~ of the ~~methods~~.	+	Dietary habits have been associated with alterations of the human gut resident microorganisms contributing to obesity, diabetes and cancer(1). In Western diets, red meat is a frequently eaten food(2), but long-term consumption has been associated with increased risk of disease(3,4). Red meat is enriched in N-glycolylneuraminic acid (Neu5Gc) that cannot be synthesized by humans(5). However, consumption can cause Neu5Gc incorporation into cell surface glycans(6), especially in carcinomas(4,7). As a consequence, an inflammatory response is triggered when Neu5Gc-containing glycans encounter circulating anti-Neu5Gc antibodies(8,9). Although bacteria can use free sialic acids as a nutrient source(10-12), it is currently unknown if gut microorganisms contribute to releasing Neu5Gc from food. We found that a Neu5Gc-rich diet induces changes in the gut microbiota, with Bacteroidales and Clostridiales responding the most. Genome assembling of mouse and human shotgun metagenomic sequencing identified bacterial sialidases with previously unobserved substrate preference for Neu5Gc-containing glycans. X-ray crystallography revealed key amino acids potentially contributing to substrate preference. Additionally, we verified that mouse and human sialidases were able to release Neu5Gc from red meat. The release of Neu5Gc from red meat using bacterial sialidases could reduce the risk of inflammatory diseases associated with red meat consumption, including colorectal cancer(4) and atherosclerosis(13).

-	~~Towards automated crystallographic structure refinement with phenix.refine~~.,~~Afonine PV~~, ~~Grosse~~-~~Kunstleve RW~~, ~~Echols N~~, ~~Headd JJ~~, ~~Moriarty NW~~, ~~Mustyakimov M~~, ~~Terwilliger TC~~, ~~Urzhumtsev A~~, ~~Zwart PH~~, ~~Adams PD Acta Crystallogr~~ D ~~Biol Crystallogr~~. ~~2012 Apr;68(Pt 4)~~:~~352~~-67. doi:, 10.~~1107~~/~~S0907444912001308. Epub 2012 Mar 16~~. PMID:~~22505256~~<ref>PMID:~~22505256~~</ref>	+	Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.,Zaramela LS, Martino C, Alisson-Silva F, Rees SD, Diaz SL, Chuzel L, Ganatra MB, Taron CH, Secrest P, Zuniga C, Huang J, Siegel D, Chang G, Varki A, Zengler K Nat Microbiol. 2019 Sep 23. pii: 10.1038/s41564-019-0564-9. doi:, 10.1038/s41564-019-0564-9. PMID:31548686<ref>PMID:31548686</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 10:27, 2 October 2019

OCA — Wed, 02 Oct 2019 10:27:27 GMT

←Older revision		Revision as of 10:27, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6myv is ~~ON HOLD until Paper~~ Publication	+	==Sialidase26 co-crystallized with DANA-Gc==
		+	<StructureSection load='6myv' size='340' side='right'caption='[[6myv]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6myv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GC9:2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic+acid'>GC9</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=6myv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myv OCA], [http://pdbe.org/6myv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myv RCSB], [http://www.ebi.ac.uk/pdbsum/6myv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myv ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

-	~~Authors: Zaramela, L~~.S., ~~Martino~~, ~~C., Alisson~~-~~Silva~~, F., ~~Rees~~, ~~S.D., Diaz, S.L., Chuzel, L., Ganatra~~, M~~.B.~~, ~~Taron~~, ~~C.H.~~, ~~Zuniga~~, C.~~, Huang, J~~., ~~Siegel, D~~.~~, Chang, G~~.~~, Varki, A., Zengler, K~~.	+	Towards automated crystallographic structure refinement with phenix.refine.,Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi:, 10.1107/S0907444912001308. Epub 2012 Mar 16. PMID:22505256<ref>PMID:22505256</ref>

-	~~Description: Sialidase26 co-crystallized with DANA-Gc~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Rees~~, S.~~D]]~~	+	<div class="pdbe-citations 6myv" style="background-color:#fffaf0;"></div>
-	~~[[Category: Taron, C~~.~~H]]~~	+	== References ==
-	~~[[Category~~: ~~Varki, A]]~~	+	<references/>
-	[[Category: ~~Zaramela, L.S~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Alisson-Silva, F]]		[[Category: Alisson-Silva, F]]
-	[[Category: Diaz, S.L]]
-	[[Category: Martino, C]]
	[[Category: Chang, G]]		[[Category: Chang, G]]
		+	[[Category: Chuzel, L]]
		+	[[Category: Diaz, S L]]
		+	[[Category: Ganatra, M B]]
	[[Category: Huang, J]]		[[Category: Huang, J]]
-	[[Category: ~~Zuniga~~, C]]	+	[[Category: Martino, C]]
-	[[Category: ~~Zengler~~, K]]	+	[[Category: Rees, S D]]
	[[Category: Siegel, D]]		[[Category: Siegel, D]]
-	[[Category: ~~Chuzel~~, L]]	+	[[Category: Taron, C H]]
-	[[Category: ~~Ganatra~~, ~~M.B~~]]	+	[[Category: Varki, A]]
		+	[[Category: Zaramela, L S]]
		+	[[Category: Zengler, K]]
		+	[[Category: Zuniga, C]]
		+	[[Category: Dana]]
		+	[[Category: Dana-gc]]
		+	[[Category: Gc]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inflammation]]
		+	[[Category: Microbiome]]
		+	[[Category: Neu5gc]]
		+	[[Category: Neu5gc2en]]
		+	[[Category: Sialic acid]]
		+	[[Category: Sialidase]]

OCA at 06:24, 30 January 2019

OCA — Wed, 30 Jan 2019 06:24:33 GMT

←Older revision		Revision as of 06:24, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zaramela, L.S., Martino, C., Alisson-Silva, F., Rees, S.D., Diaz, S.L., Chuzel, L., Ganatra, M.B., Taron, C.H., Zuniga, C., Huang, J., Siegel, D., Chang, G., Varki, A., Zengler, K.		Authors: Zaramela, L.S., Martino, C., Alisson-Silva, F., Rees, S.D., Diaz, S.L., Chuzel, L., Ganatra, M.B., Taron, C.H., Zuniga, C., Huang, J., Siegel, D., Chang, G., Varki, A., Zengler, K.

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

OCA — Wed, 14 Nov 2018 06:40:29 GMT

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

←Older revision

Revision as of 06:40, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6myv is ON HOLD Authors: Zaramela, L.S., Martino, C., Alisson-Silva, F., Rees, S.D., Diaz, S.L., Chuzel, L., Ganatra, M.B., Taron, C.H., Zuniga, C.,...

OCA — Wed, 14 Nov 2018 06:40:28 GMT

New page: '''Unreleased structure''' The entry 6myv is ON HOLD Authors: Zaramela, L.S., Martino, C., Alisson-Silva, F., Rees, S.D., Diaz, S.L., Chuzel, L., Ganatra, M.B., Taron, C.H., Zuniga, C.,...

New page

'''Unreleased structure'''

The entry 6myv is ON HOLD

Authors: Zaramela, L.S., Martino, C., Alisson-Silva, F., Rees, S.D., Diaz, S.L., Chuzel, L., Ganatra, M.B., Taron, C.H., Zuniga, C., Huang, J., Siegel, D., Chang, G., Varki, A., Zengler, K.

Description: Sialidase26 co-crystallized with DANA-Gc
[[Category: Unreleased Structures]]
[[Category: Rees, S.D]]
[[Category: Taron, C.H]]
[[Category: Varki, A]]
[[Category: Zaramela, L.S]]
[[Category: Alisson-Silva, F]]
[[Category: Diaz, S.L]]
[[Category: Martino, C]]
[[Category: Chang, G]]
[[Category: Huang, J]]
[[Category: Zuniga, C]]
[[Category: Zengler, K]]
[[Category: Siegel, D]]
[[Category: Chuzel, L]]
[[Category: Ganatra, M.B]]