1p46 - Revision history

OCA at 09:37, 16 August 2023

OCA — Wed, 16 Aug 2023 09:37:06 GMT

←Older revision		Revision as of 09:37, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1p46' size='340' side='right'caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='1p46' size='340' side='right'caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p46]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p46]] 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=1P46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P46 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=HED:2~~-~~HYDROXYETHYL+DISULFIDE'>HED</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.67Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]~~</~~div~~><~~/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=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [https://pdbe.org/1p46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [https://www.ebi.ac.uk/pdbsum/1p46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p46 ProSAT]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [https://pdbe.org/1p46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [https://www.ebi.ac.uk/pdbsum/1p46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p46 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~LYS_BPT4 LYS_BPT4~~]~~] Helps~~ to ~~release~~ the mature ~~phage~~ particles ~~from~~ the cell ~~wall by breaking~~ down the peptidoglycan.	+	[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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Baase WA]]
-	[[Category: Baase~~, W A~~]]	+	[[Category: Datta D]]
-	[[Category: Datta, D]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W~~]]	+	[[Category: Mayo SL]]
-	[[Category: Mayo~~, S L~~]]	+	[[Category: Mooers BH]]
-	[[Category: Mooers~~, B H~~]]	+	[[Category: Zollars ES]]
-	[[Category: Zollars~~, E S]]~~	+
-	~~[[Category: Automated protein design]]~~	+
-	~~[[Category: Back revertant]]~~	+
-	~~[[Category: Core repacking]]~~	+
-	~~[[Category: Dead-end elimination theorem]]~~	+
-	~~[[Category: Designed core mutant]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Optimized rotamer combination]]~~	+
-	~~[[Category: Orbit]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: Protein folding]]~~	+
-	~~[[Category: Protein stability]]~~	+
-	~~[[Category: Side-chain packing]]~~	+
-	~~[[Category: T4 lysozyme~~]]	+

OCA at 09:25, 8 September 2021

OCA — Wed, 08 Sep 2021 09:25:04 GMT

←Older revision		Revision as of 09:25, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1p46' size='340' side='right'caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='1p46' size='340' side='right'caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p46]] 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=1P46 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1P46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p46]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P46 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=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</div></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'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [~~http~~://pdbe.org/1p46 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1p46 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1p46 ProSAT]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [https://pdbe.org/1p46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [https://www.ebi.ac.uk/pdbsum/1p46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p46 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.	+	[[https://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:22, 27 November 2019

OCA — Wed, 27 Nov 2019 10:22:01 GMT

←Older revision		Revision as of 10:22, 27 November 2019
Line 1:		Line 1:

	==T4 lysozyme core repacking mutant M106I/TA==		==T4 lysozyme core repacking mutant M106I/TA==
-	<StructureSection load='1p46' size='340' side='right' caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>	+	<StructureSection load='1p46' size='340' side='right'caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1p46]] 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=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1p46]] 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=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1p46" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1p46" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 07:51, 15 February 2018

OCA — Thu, 15 Feb 2018 07:51:06 GMT

←Older revision		Revision as of 07:51, 15 February 2018
Line 1:		Line 1:
		+
	==T4 lysozyme core repacking mutant M106I/TA==		==T4 lysozyme core repacking mutant M106I/TA==
	<StructureSection load='1p46' size='340' side='right' caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='1p46' size='340' side='right' caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://pdbe.org/1p46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://pdbe.org/1p46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p46 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p46_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p46_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1p46 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1p46" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1p46" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:02, 11 September 2015

OCA — Fri, 11 Sep 2015 17:02:18 GMT

←Older revision		Revision as of 17:02, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1p46' size='340' side='right' caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='1p46' size='340' side='right' caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p46]] 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=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 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=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://pdbe.org/1p46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 1p46" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 19:21, 25 December 2014

OCA — Thu, 25 Dec 2014 19:21:06 GMT

←Older revision		Revision as of 19:21, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1p46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1p46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><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=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum]</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=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Baase, W A.]]	+	[[Category: Baase, W A]]
-	[[Category: Datta, D.]]	+	[[Category: Datta, D]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
-	[[Category: Mayo, S L.]]	+	[[Category: Mayo, S L]]
-	[[Category: Mooers, B H.]]	+	[[Category: Mooers, B H]]
-	[[Category: Zollars, E S.]]	+	[[Category: Zollars, E S]]
	[[Category: Automated protein design]]		[[Category: Automated protein design]]
	[[Category: Back revertant]]		[[Category: Back revertant]]

OCA at 19:47, 28 September 2014

OCA — Sun, 28 Sep 2014 19:47:18 GMT

←Older revision		Revision as of 19:47, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1p46.~~png~~\|~~left~~\|200px]]	+	==T4 lysozyme core repacking mutant M106I/TA==
		+	<StructureSection load='1p46' size='340' side='right' caption='[[1p46]], [[Resolution\|resolution]] 1.67Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1p46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P46 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p46 RCSB], [http://www.ebi.ac.uk/pdbsum/1p46 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p46_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Automated protein redesign, as implemented in the program ORBIT, was used to redesign the core of phage T4 lysozyme. A total of 26 buried or partially buried sites in the C-terminal domain were allowed to vary both their sequence and side-chain conformation while the backbone and non-selected side-chains remained fixed. A variant with seven substitutions ("Core-7") was identified as having the most favorable energy. The redesign experiment was repeated with a penalty for the presence of methionine residues. In this case the redesigned protein ("Core-10") had ten amino acid changes. The two designed proteins, as well as the constituent single mutants, and several single-site revertants were over-expressed in Escherichia coli, purified, and subjected to crystallographic and thermal analyses. The thermodynamic and structural data show that some repacking was achieved although neither redesigned protein was more stable than the wild-type protein. The use of the methionine penalty was shown to be effective. Several of the side-chain rotamers in the predicted structure of Core-10 differ from those observed. Rather than changing to new rotamers predicted by the design process, side-chains tend to maintain conformations similar to those seen in the native molecule. In contrast, parts of the backbone change by up to 2.8A relative to both the designed structure and wild-type.Water molecules that are present within the lysozyme molecule were removed during the design process. In the redesigned protein the resultant cavities were, to some degree, re-occupied by side-chain atoms. In the observed structure, however, water molecules were still bound at or near their original sites. This suggests that it may be preferable to leave such water molecules in place during the design procedure. The results emphasize the specificity of the packing that occurs within the core of a typical protein. While point substitutions within the core are tolerated they almost always result in a loss of stability. Likewise, combinations of substitutions may also be tolerated but usually destabilize the protein. Experience with T4 lysozyme suggests that a general core repacking methodology with retention or enhancement of stability may be difficult to achieve without provision for shifts in the backbone.

-	~~{{STRUCTURE_1p46\| PDB=1p46 \| SCENE= }}~~	+	Repacking the Core of T4 lysozyme by automated design.,Mooers BH, Datta D, Baase WA, Zollars ES, Mayo SL, Matthews BW J Mol Biol. 2003 Sep 19;332(3):741-56. PMID:12963380<ref>PMID:12963380</ref>

-	~~===T4 lysozyme core repacking mutant M106I~~/~~TA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12963380}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1p46]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012963380<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 20:29, 20 October 2012

OCA — Sat, 20 Oct 2012 20:29:07 GMT

←Older revision		Revision as of 20:29, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1p46]] is a 1 chain structure ~~of [[Hen Egg-White (HEW) Lysozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA].	+	[[1p46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA].

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

OCA: Protected "1p46" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 10:37:21 GMT

Protected "1p46" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:37, 27 July 2012

OCA at 10:37, 27 July 2012

OCA — Fri, 27 Jul 2012 10:37:19 GMT

←Older revision		Revision as of 10:37, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1p46.png\|left\|200px]]		[[Image:1p46.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1p46", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1p46\| PDB=1p46 \| SCENE= }}		{{STRUCTURE_1p46\| PDB=1p46 \| SCENE= }}

	===T4 lysozyme core repacking mutant M106I/TA===		===T4 lysozyme core repacking mutant M106I/TA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12963380}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12963380 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12963380}}		{{ABSTRACT_PUBMED_12963380}}

	==About this Structure==		==About this Structure==
-	~~1P46~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA].	+	[[1p46]] is a 1 chain structure of [[Hen Egg-White (HEW) Lysozyme]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P46 OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12963380~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012963380</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 37:		Line 28:
	[[Category: Dead-end elimination theorem]]		[[Category: Dead-end elimination theorem]]
	[[Category: Designed core mutant]]		[[Category: Designed core mutant]]
		+	[[Category: Hydrolase]]
	[[Category: Optimized rotamer combination]]		[[Category: Optimized rotamer combination]]
	[[Category: Orbit]]		[[Category: Orbit]]
Line 44:		Line 36:
	[[Category: Side-chain packing]]		[[Category: Side-chain packing]]
	[[Category: T4 lysozyme]]		[[Category: T4 lysozyme]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:19:52 2009''