5vnq - Revision history

OCA at 13:52, 4 October 2023

OCA — Wed, 04 Oct 2023 13:52:30 GMT

←Older revision		Revision as of 13:52, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5vnq' size='340' side='right'caption='[[5vnq]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5vnq' size='340' side='right'caption='[[5vnq]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vnq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VNQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vnq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VNQ FirstGlance]. <br>
-	</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=DOD:DEUTERATED+WATER'>DOD</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution\|Resolution]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5vnr\|5vnr~~]]</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=DOD:DEUTERATED+WATER'>DOD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>e, T4Tp126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~10665 BPT4])</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=5vnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnq OCA], [https://pdbe.org/5vnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vnq RCSB], [https://www.ebi.ac.uk/pdbsum/5vnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnq ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5vnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnq OCA], [~~http~~://pdbe.org/5vnq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vnq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vnq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</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 5vnq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vnq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysin 3D structures\|Lysin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Cuneo MJ]]
-	[[Category: Cuneo~~, M J~~]]	+	[[Category: Li L]]
-	[[Category: Li, L]]	+	[[Category: Meilleur F]]
-	[[Category: Meilleur, F]]	+	[[Category: Myles DAA]]
-	[[Category: Myles~~, D A.A~~]]	+	[[Category: Pierce J]]
-	[[Category: Pierce, J]]	+	[[Category: Shukla S]]
-	[[Category: Shukla, S]]	+	[[Category: Standaert RF]]
-	[[Category: Standaert~~, R F]]~~	+
-	~~[[Category: Hydrogen bond]]~~	+
-	~~[[Category: Hydrogen bonding network]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Neutron crystallography]]~~	+
-	~~[[Category: T4 lysozyme]]~~	+
-	~~[[Category: Water~~]]	+

OCA at 09:45, 9 September 2020

OCA — Wed, 09 Sep 2020 09:45:48 GMT

←Older revision		Revision as of 09:45, 9 September 2020
Line 1:		Line 1:

-	==Neutron crystallographic ~~strucutre~~ of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature==	+	==Neutron crystallographic structure of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature==
-	<StructureSection load='5vnq' size='340' side='right' caption='[[5vnq]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5vnq' size='340' side='right'caption='[[5vnq]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vnq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VNQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vnq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VNQ 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=DOD:DEUTERATED+WATER'>DOD</scene></td></tr>	+	</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=DOD:DEUTERATED+WATER'>DOD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vnr\|5vnr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vnr\|5vnr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">e, T4Tp126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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='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=5vnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnq OCA], [http://pdbe.org/5vnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vnq RCSB], [http://www.ebi.ac.uk/pdbsum/5vnq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnq 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=5vnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnq OCA], [http://pdbe.org/5vnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vnq RCSB], [http://www.ebi.ac.uk/pdbsum/5vnq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Cuneo, M J]]		[[Category: Cuneo, M J]]

OCA at 09:08, 4 October 2017

OCA — Wed, 04 Oct 2017 09:08:51 GMT

←Older revision		Revision as of 09:08, 4 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vnq is ~~ON HOLD~~	+	==Neutron crystallographic strucutre of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature==
		+	<StructureSection load='5vnq' size='340' side='right' caption='[[5vnq]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vnq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VNQ 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=DOD:DEUTERATED+WATER'>DOD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vnr\|5vnr]]</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='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=5vnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnq OCA], [http://pdbe.org/5vnq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vnq RCSB], [http://www.ebi.ac.uk/pdbsum/5vnq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X-ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 A-resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo-wild type. We describe a near complete atomic structure of T4L, which includes the positions of 1737 hydrogen atoms determined by neutron crystallography. The cryogenic neutron model reveals explicit detail of the hydrogen bonding interactions in the protein, in addition to the protonation states of several important residues.

-	~~Authors: Li~~, L. , Shukla, S., Meilleur, F., Standaert~~, R.F.~~, Pierce, J., Myles, D.A.A.~~, Cuneo, M~~.J.	+	Neutron crystallographic studies of T4 lysozyme at cryogenic temperature.,Li L, Shukla S, Meilleur F, Standaert RF, Pierce J, Myles DAA, Cuneo MJ Protein Sci. 2017 Oct;26(10):2098-2104. doi: 10.1002/pro.3231. Epub 2017 Sep 6. PMID:28707382<ref>PMID:28707382</ref>

-	~~Description: Neutron crystallographic strucutre~~ of ~~perdeuterated T4 lysozyme cysteine~~-~~free pseudo~~-~~wild type at cryogenic temperature~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vnq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysozyme]]
		+	[[Category: Cuneo, M J]]
		+	[[Category: Li, L]]
	[[Category: Meilleur, F]]		[[Category: Meilleur, F]]
-	[[Category: Li, L. ~~, Shukla, S~~]]	+	[[Category: Myles, D A.A]]
	[[Category: Pierce, J]]		[[Category: Pierce, J]]
-	[[Category: ~~Cuneo~~, ~~M.J~~]]	+	[[Category: Shukla, S]]
-	[[Category: Standaert, R.F]]	+	[[Category: Standaert, R F]]
-	[[Category: ~~Myles, D.A.A~~]]	+	[[Category: Hydrogen bond]]
		+	[[Category: Hydrogen bonding network]]
		+	[[Category: Hydrolase]]
		+	[[Category: Neutron crystallography]]
		+	[[Category: T4 lysozyme]]
		+	[[Category: Water]]

OCA: Protected "5vnq" [edit=sysop:move=sysop]

OCA — Wed, 10 May 2017 11:13:52 GMT

Protected "5vnq" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:13, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vnq is ON HOLD Authors: Li, L. , Shukla, S., Meilleur, F., Standaert, R.F., Pierce, J., Myles, D.A.A., Cuneo, M.J. Description: Neutron crystallog...

OCA — Wed, 10 May 2017 11:13:51 GMT

New page: '''Unreleased structure''' The entry 5vnq is ON HOLD Authors: Li, L. , Shukla, S., Meilleur, F., Standaert, R.F., Pierce, J., Myles, D.A.A., Cuneo, M.J. Description: Neutron crystallog...

New page

'''Unreleased structure'''

The entry 5vnq is ON HOLD

Authors: Li, L. , Shukla, S., Meilleur, F., Standaert, R.F., Pierce, J., Myles, D.A.A., Cuneo, M.J.

Description: Neutron crystallographic strucutre of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature
[[Category: Unreleased Structures]]
[[Category: Meilleur, F]]
[[Category: Li, L. , Shukla, S]]
[[Category: Pierce, J]]
[[Category: Cuneo, M.J]]
[[Category: Standaert, R.F]]
[[Category: Myles, D.A.A]]