5kio - Revision history

OCA at 10:01, 27 September 2023

2023-09-27T10:01:36Z

←Older revision		Revision as of 10:01, 27 September 2023
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	<StructureSection load='5kio' size='340' side='right'caption='[[5kio]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='5kio' size='340' side='right'caption='[[5kio]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kio]] 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=5KIO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kio]] 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=5KIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KIO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=HED:2~~-~~HYDROXYETHYL+DISULFIDE'>HED</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]] 1.63Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PHI~~:~~IODO~~-~~PHENYLALANINE~~'>~~PHI~~</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5khz\|5khz]]~~, ~~[[5ki1\|5ki1]], [[5ki2\|5ki2]], [[5ki3\|5ki3]], [[5ki8\|5ki8]], [[5kig\|5kig]], [[5kii\|5kii]], [[5kim\|5kim]]~~<~~/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=5kio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kio OCA], [https://pdbe.org/5kio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kio RCSB], [https://www.ebi.ac.uk/pdbsum/5kio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kio 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5kio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kio OCA], [~~http~~://pdbe.org/5kio PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kio RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kio PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kio ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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>	+	[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 ==
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	</div>		</div>
	<div class="pdbe-citations 5kio" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kio" 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: Scholfield MR]]
-	[[Category: Scholfield~~, M R]]~~	+
-	~~[[Category: Halogen bond]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: T4 lysozyme~~]]	+

OCA at 07:44, 27 November 2019

2019-11-27T07:44:46Z

←Older revision		Revision as of 07:44, 27 November 2019
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	==PSEUDO T4 LYSOZYME MUTANT - Y18PHE-I==		==PSEUDO T4 LYSOZYME MUTANT - Y18PHE-I==
-	<StructureSection load='5kio' size='340' side='right' caption='[[5kio]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='5kio' size='340' side='right'caption='[[5kio]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kio]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kio]] 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=5KIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Scholfield, M R]]		[[Category: Scholfield, M R]]

OCA at 06:02, 19 April 2017

2017-04-19T06:02:06Z

←Older revision		Revision as of 06:02, 19 April 2017
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	== Function ==		== Function ==
	[[http://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>		[[http://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;">
		+	== Publication Abstract from PubMed ==
		+	The structures and stabilities of proteins are defined by a series of weak non-covalent electrostatic, van der Waals, and hydrogen bond (HB) interactions. In this study, we have designed and engineered halogen bonds (XBs) site-specifically in order to study their structure-energy relationship in a model protein, T4 lysozyme. The evidence for XBs is the displacement of the aromatic side chain towards an oxygen acceptor, at distances that are at or less than the sums of their respective van der Waals radii, when the hydroxyl substituent of the wildtype tyrosine is replaced by an iodine. In addition, thermal melting studies show that the iodine XB rescues the stabilization energy from an otherwise destabilizing substitution (at an equivalent non-interacting site), indicating that the interaction is also present in solution. Quantum chemical calculations show that the XB complements an HB at this site and that solvent structure must also be considered in trying to design molecular interactions such as XBs into biological systems. A bromine substitution also shows displacement of the side chain, but the distances and geometries do not indicate formation of an XB. Thus, we have dissected the contributions from various non-covalent interactions of halogens introduced into proteins, to drive the application of XBs, particularly in biomolecular design.
		+
		+	Structure-Energy Relationships of Halogen Bonds in Proteins.,Scholfield MR, Ford MC, Carlsson AC, Butta H, Mehl RA, Ho PS Biochemistry. 2017 Mar 27. doi: 10.1021/acs.biochem.7b00022. PMID:28345933<ref>PMID:28345933</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kio" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:44, 12 April 2017

2017-04-12T11:44:10Z

←Older revision		Revision as of 11:44, 12 April 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5kio is ~~ON HOLD~~ ~~until Paper Publication~~	+	==PSEUDO T4 LYSOZYME MUTANT - Y18PHE-I==
-		+	<StructureSection load='5kio' size='340' side='right' caption='[[5kio]], [[Resolution\|resolution]] 1.63Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kio]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIO FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5khz\|5khz]], [[5ki1\|5ki1]], [[5ki2\|5ki2]], [[5ki3\|5ki3]], [[5ki8\|5ki8]], [[5kig\|5kig]], [[5kii\|5kii]], [[5kim\|5kim]]</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=5kio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kio OCA], [http://pdbe.org/5kio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kio RCSB], [http://www.ebi.ac.uk/pdbsum/5kio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kio ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysozyme]]
		+	[[Category: Scholfield, M R]]
		+	[[Category: Halogen bond]]
		+	[[Category: Hydrolase]]
		+	[[Category: T4 lysozyme]]

OCA at 13:01, 27 July 2016

2016-07-27T13:01:24Z

←Older revision		Revision as of 13:01, 27 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kio is ON HOLD	+	The entry 5kio is ON HOLD until Paper Publication

	Authors:		Authors:

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

2016-06-23T21:40:54Z

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

←Older revision

Revision as of 21:40, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kio is ON HOLD Authors: Description: Category: Unreleased Structures

2016-06-23T21:40:52Z

New page: '''Unreleased structure''' The entry 5kio is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kio is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]