5lwo - Revision history

OCA at 06:55, 3 April 2024

2024-04-03T06:55:13Z

←Older revision		Revision as of 06:55, 3 April 2024
Line 10:		Line 10:
	== Function ==		== 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>		[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;">
-	== Publication Abstract from PubMed ==
-	Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.
-
-	Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins.,Consentius P, Loll B, Gohlke U, Alings C, Muller C, Muller R, Teutloff C, Heinemann U, Kaupp M, Wahl MC, Risse T J Phys Chem Lett. 2017 Feb 23:1113-1117. doi: 10.1021/acs.jpclett.6b02971. PMID:28221042<ref>PMID:28221042</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5lwo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 18:53, 18 October 2023

2023-10-18T18:53:53Z

←Older revision		Revision as of 18:53, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='5lwo' size='340' side='right'caption='[[5lwo]], [[Resolution\|resolution]] 1.18Å' scene=''>		<StructureSection load='5lwo' size='340' side='right'caption='[[5lwo]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lwo]] 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=5LWO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lwo]] 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=5LWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LWO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RXR:[2,2,5,5-TETRAMETHYL-3,4-BIS(SULFANYLMETHYL)-2,5-DIHYDRO-1H-PYRROL-1-YL]OXIDANYL+RADICAL'>RXR</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]] 1.183Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdt\|5jdt]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RXR:[2,2,5,5-TETRAMETHYL-3,4-BIS(SULFANYLMETHYL)-2,5-DIHYDRO-1H-PYRROL-1-YL]OXIDANYL+RADICAL'>RXR</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5lwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lwo OCA], [https://pdbe.org/5lwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lwo RCSB], [https://www.ebi.ac.uk/pdbsum/5lwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lwo ProSAT]</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=5lwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lwo OCA], [~~http~~://pdbe.org/5lwo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lwo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lwo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lwo 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 ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5lwo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lwo" 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: Consentius P]]
-	[[Category: Consentius, P]]	+	[[Category: Gohlke U]]
-	[[Category: Gohlke, U]]	+	[[Category: Heinemann U]]
-	[[Category: Heinemann, U]]	+	[[Category: Kaupp M]]
-	[[Category: Kaupp, M]]	+	[[Category: Loll B]]
-	[[Category: Loll, B]]	+	[[Category: Mueller R]]
-	[[Category: Mueller, R]]	+	[[Category: Risse T]]
-	[[Category: Risse, T]]	+	[[Category: Wahl MC]]
-	[[Category: Wahl~~, M C]]~~	+
-	~~[[Category: Electron paramagnetic resonance]]~~	+
-	~~[[Category: Epr]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nitroxide]]~~	+
-	~~[[Category: Spin label]]~~	+
-	~~[[Category: T4 lysozyme~~]]	+

OCA at 06:02, 12 June 2019

2019-06-12T06:02:03Z

←Older revision		Revision as of 06:02, 12 June 2019
Line 1:		Line 1:

	==Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K==		==Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K==
-	<StructureSection load='5lwo' size='340' side='right' caption='[[5lwo]], [[Resolution\|resolution]] 1.18Å' scene=''>	+	<StructureSection load='5lwo' size='340' side='right'caption='[[5lwo]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lwo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lwo]] 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=5LWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LWO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RXR:[2,2,5,5-TETRAMETHYL-3,4-BIS(SULFANYLMETHYL)-2,5-DIHYDRO-1H-PYRROL-1-YL]OXIDANYL+RADICAL'>RXR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RXR:[2,2,5,5-TETRAMETHYL-3,4-BIS(SULFANYLMETHYL)-2,5-DIHYDRO-1H-PYRROL-1-YL]OXIDANYL+RADICAL'>RXR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdt\|5jdt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdt\|5jdt]]</td></tr>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: ~~CONSENTIUS~~, P]]	+	[[Category: Consentius, P]]
-	[[Category: ~~GOHLKE~~, U]]	+	[[Category: Gohlke, U]]
	[[Category: Heinemann, U]]		[[Category: Heinemann, U]]
-	[[Category: ~~KAUPP~~, M]]	+	[[Category: Kaupp, M]]
	[[Category: Loll, B]]		[[Category: Loll, B]]
-	[[Category: ~~MUELLER~~, R]]	+	[[Category: Mueller, R]]
	[[Category: Risse, T]]		[[Category: Risse, T]]
	[[Category: Wahl, M C]]		[[Category: Wahl, M C]]

OCA at 16:46, 9 March 2017

2017-03-09T16:46:32Z

←Older revision		Revision as of 16:46, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lwo is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K==
		+	<StructureSection load='5lwo' size='340' side='right' caption='[[5lwo]], [[Resolution\|resolution]] 1.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lwo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LWO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RXR:[2,2,5,5-TETRAMETHYL-3,4-BIS(SULFANYLMETHYL)-2,5-DIHYDRO-1H-PYRROL-1-YL]OXIDANYL+RADICAL'>RXR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdt\|5jdt]]</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=5lwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lwo OCA], [http://pdbe.org/5lwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lwo RCSB], [http://www.ebi.ac.uk/pdbsum/5lwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lwo 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.

-	~~Authors~~:	+	Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins.,Consentius P, Loll B, Gohlke U, Alings C, Muller C, Muller R, Teutloff C, Heinemann U, Kaupp M, Wahl MC, Risse T J Phys Chem Lett. 2017 Feb 23:1113-1117. doi: 10.1021/acs.jpclett.6b02971. PMID:28221042<ref>PMID:28221042</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5lwo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysozyme]]
		+	[[Category: CONSENTIUS, P]]
		+	[[Category: GOHLKE, U]]
		+	[[Category: Heinemann, U]]
		+	[[Category: KAUPP, M]]
		+	[[Category: Loll, B]]
		+	[[Category: MUELLER, R]]
		+	[[Category: Risse, T]]
		+	[[Category: Wahl, M C]]
		+	[[Category: Electron paramagnetic resonance]]
		+	[[Category: Epr]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nitroxide]]
		+	[[Category: Spin label]]
		+	[[Category: T4 lysozyme]]

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

2016-10-03T14:47:56Z

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

←Older revision

Revision as of 14:47, 3 October 2016

OCA: New page: '''Unreleased structure''' The entry 5lwo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-10-03T14:47:55Z

New page: '''Unreleased structure''' The entry 5lwo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5lwo is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]