5jgr - Revision history

OCA at 07:24, 1 May 2024

OCA — Wed, 01 May 2024 07:24:23 GMT

←Older revision		Revision as of 07:24, 1 May 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 ==
-	Pulsed electron paramagnetic resonance experiments can measure individual distances between two spin-labeled side chains in proteins in the range of approximately 1.5-8 nm. However, the flexibility of traditional spin-labeled side chains leads to diffuse spin density loci and thus distance distributions with relatively broad peaks, thereby complicating the interpretation of protein conformational states. Here we analyzed the spin-labeled V1 side chain, which is internally anchored and hence less flexible. Crystal structures of V1-labeled T4 lysozyme constructs carrying the V1 side chain on alpha-helical segments suggest that V1 side chains adopt only a few discrete rotamers. In most cases, only one rotamer is observed at a given site, explaining the frequently observed narrow distance distribution for doubly V1-labeled proteins. We used the present data to derive guidelines that may allow distance interpretation of other V1-labeled proteins for higher-precision structural modeling.
-
-	Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains.,Balo AR, Feyrer H, Ernst OP Biochemistry. 2016 Sep 20;55(37):5256-63. doi: 10.1021/acs.biochem.6b00608. Epub , 2016 Sep 2. PMID:27532325<ref>PMID:27532325</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5jgr" style="background-color:#fffaf0;"></div>

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

OCA at 18:51, 20 September 2023

OCA — Wed, 20 Sep 2023 18:51:20 GMT

←Older revision		Revision as of 18:51, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jgr' size='340' side='right'caption='[[5jgr]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='5jgr' size='340' side='right'caption='[[5jgr]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jgr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4_sensu_lato Enterobacteria~~ phage ~~t4 sensu lato~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jgr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T4 Escherichia phage T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JGR 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=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V1A:S-(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)+METHANESULFONOTHIOATE'>V1A</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]] 1.46Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jgn\|5jgn]], [[5jgu\|5jgu]], [[5jgv\|5jgv]], [[5jgx\|5jgx]], [[5jgz\|5jgz]]</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=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V1A:S-(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)+METHANESULFONOTHIOATE'>V1A</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=5jgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgr OCA], [https://pdbe.org/5jgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jgr RCSB], [https://www.ebi.ac.uk/pdbsum/5jgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgr 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=5jgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgr OCA], [~~http~~://pdbe.org/5jgr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jgr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jgr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgr 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 5jgr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jgr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysin 3D structures\|Lysin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria~~ phage ~~t4 sensu lato~~]]	+	[[Category: Escherichia phage T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Balo AR]]
-	[[Category: Balo~~, A R~~]]	+	[[Category: Ernst OP]]
-	[[Category: Ernst~~, O P~~]]	+	[[Category: Feyrer H]]
-	[[Category: Feyrer, H]]	+
-	~~[[Category: Deer]]~~	+
-	~~[[Category: Epr]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Spin label~~]]	+

OCA at 08:06, 8 January 2020

OCA — Wed, 08 Jan 2020 08:06:49 GMT

←Older revision		Revision as of 08:06, 8 January 2020
Line 1:		Line 1:

	==Spin-Labeled T4 Lysozyme Construct K43V1==		==Spin-Labeled T4 Lysozyme Construct K43V1==
-	<StructureSection load='5jgr' size='340' side='right' caption='[[5jgr]], [[Resolution\|resolution]] 1.46Å' scene=''>	+	<StructureSection load='5jgr' size='340' side='right'caption='[[5jgr]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jgr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4_sensu_lato Enterobacteria phage t4 sensu lato]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGR 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=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V1A:S-(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)+METHANESULFONOTHIOATE'>V1A</scene></td></tr>		</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=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V1A:S-(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)+METHANESULFONOTHIOATE'>V1A</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jgn\|5jgn]], [[5jgu\|5jgu]], [[5jgv\|5jgv]], [[5jgx\|5jgx]], [[5jgz\|5jgz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jgn\|5jgn]], [[5jgu\|5jgu]], [[5jgv\|5jgv]], [[5jgx\|5jgx]], [[5jgz\|5jgz]]</td></tr>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterobacteria phage t4 sensu lato]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Balo, A R]]		[[Category: Balo, A R]]

OCA at 07:05, 25 October 2017

OCA — Wed, 25 Oct 2017 07:05:20 GMT

←Older revision		Revision as of 07:05, 25 October 2017
Line 11:		Line 11:
	== 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 ==
		+	Pulsed electron paramagnetic resonance experiments can measure individual distances between two spin-labeled side chains in proteins in the range of approximately 1.5-8 nm. However, the flexibility of traditional spin-labeled side chains leads to diffuse spin density loci and thus distance distributions with relatively broad peaks, thereby complicating the interpretation of protein conformational states. Here we analyzed the spin-labeled V1 side chain, which is internally anchored and hence less flexible. Crystal structures of V1-labeled T4 lysozyme constructs carrying the V1 side chain on alpha-helical segments suggest that V1 side chains adopt only a few discrete rotamers. In most cases, only one rotamer is observed at a given site, explaining the frequently observed narrow distance distribution for doubly V1-labeled proteins. We used the present data to derive guidelines that may allow distance interpretation of other V1-labeled proteins for higher-precision structural modeling.
		+
		+	Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains.,Balo AR, Feyrer H, Ernst OP Biochemistry. 2016 Sep 20;55(37):5256-63. doi: 10.1021/acs.biochem.6b00608. Epub , 2016 Sep 2. PMID:27532325<ref>PMID:27532325</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jgr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:39, 10 March 2017

OCA — Fri, 10 Mar 2017 17:39:54 GMT

←Older revision		Revision as of 17:39, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jgr is ~~ON HOLD until Paper Publication~~	+	==Spin-Labeled T4 Lysozyme Construct K43V1==
-		+	<StructureSection load='5jgr' size='340' side='right' caption='[[5jgr]], [[Resolution\|resolution]] 1.46Å' scene=''>
-	~~Authors~~: ~~Balo~~, A.R., ~~Feyrer~~, H., ~~Ernst~~, O.P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jgr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGR FirstGlance]. <br>
-	~~Description~~: ~~Spin~~-~~Labeled T4 Lysozyme Construct K43V1~~	+	</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=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V1A:S-(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)+METHANESULFONOTHIOATE'>V1A</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jgn\|5jgn]], [[5jgu\|5jgu]], [[5jgv\|5jgv]], [[5jgx\|5jgx]], [[5jgz\|5jgz]]</td></tr>
-	[[Category: ~~Ernst, O.P~~]]	+	<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>
-	[[Category: Balo, A.R]]	+	<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=5jgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgr OCA], [http://pdbe.org/5jgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jgr RCSB], [http://www.ebi.ac.uk/pdbsum/5jgr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgr 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: Balo, A R]]
		+	[[Category: Ernst, O P]]
	[[Category: Feyrer, H]]		[[Category: Feyrer, H]]
		+	[[Category: Deer]]
		+	[[Category: Epr]]
		+	[[Category: Hydrolase]]
		+	[[Category: Spin label]]

OCA at 08:16, 14 July 2016

OCA — Thu, 14 Jul 2016 08:16:24 GMT

←Older revision		Revision as of 08:16, 14 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Balo, A.R., Feyrer, H., Ernst, O.P.		Authors: Balo, A.R., Feyrer, H., Ernst, O.P.

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

OCA — Wed, 11 May 2016 02:02:08 GMT

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

←Older revision

Revision as of 02:02, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jgr is ON HOLD Authors: Balo, A.R., Feyrer, H., Ernst, O.P. Description: Spin-Labeled T4 Lysozyme Construct K43V1 [[Category: Unreleased Structure...

OCA — Wed, 11 May 2016 02:02:07 GMT

New page: '''Unreleased structure''' The entry 5jgr is ON HOLD Authors: Balo, A.R., Feyrer, H., Ernst, O.P. Description: Spin-Labeled T4 Lysozyme Construct K43V1 [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 5jgr is ON HOLD

Authors: Balo, A.R., Feyrer, H., Ernst, O.P.

Description: Spin-Labeled T4 Lysozyme Construct K43V1
[[Category: Unreleased Structures]]
[[Category: Ernst, O.P]]
[[Category: Balo, A.R]]
[[Category: Feyrer, H]]