1pqi - Revision history

OCA at 09:46, 16 August 2023

OCA — Wed, 16 Aug 2023 09:46:15 GMT

←Older revision		Revision as of 09:46, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1pqi' size='340' side='right'caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1pqi' size='340' side='right'caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQI FirstGlance]. <br>
-	</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=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]] 1.57Å</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]~~</~~div~~><~~/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=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">E ([https://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~~'>~~[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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [https://pdbe.org/1pqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [https://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi 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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [https://pdbe.org/1pqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [https://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi 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 38:		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 15:16, 27 October 2021

OCA — Wed, 27 Oct 2021 15:16:17 GMT

OCA at 07:34, 9 December 2020

OCA — Wed, 09 Dec 2020 07:34:07 GMT

←Older revision		Revision as of 07:34, 9 December 2020
Line 1:		Line 1:

	==T4 LYSOZYME CORE REPACKING MUTANT I118L/CORE7/TA==		==T4 LYSOZYME CORE REPACKING MUTANT I118L/CORE7/TA==
-	<StructureSection load='1pqi' size='340' side='right' caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='1pqi' size='340' side='right'caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PQI 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=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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://pdbe.org/1pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi 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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://pdbe.org/1pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1pqi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pqi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 08:17, 24 February 2018

OCA — Sat, 24 Feb 2018 08:17:14 GMT

←Older revision		Revision as of 08:17, 24 February 2018
Line 1:		Line 1:
		+
	==T4 LYSOZYME CORE REPACKING MUTANT I118L/CORE7/TA==		==T4 LYSOZYME CORE REPACKING MUTANT I118L/CORE7/TA==
	<StructureSection load='1pqi' size='340' side='right' caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1pqi' size='340' side='right' caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://pdbe.org/1pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi 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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://pdbe.org/1pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pq/1pqi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pq/1pqi_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>
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1pqi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pqi" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:48, 8 February 2016

OCA — Mon, 08 Feb 2016 23:48:08 GMT

←Older revision		Revision as of 23:48, 8 February 2016
Line 19:		Line 19:
	<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=1pqi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:32, 10 September 2015

OCA — Thu, 10 Sep 2015 16:32:58 GMT

←Older revision		Revision as of 16:32, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1pqi' size='340' side='right' caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1pqi' size='340' side='right' caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PQI 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=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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 ~~Enterobacteria phage T4~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi 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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://pdbe.org/1pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1pqi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 02:59, 25 December 2014

OCA — Thu, 25 Dec 2014 02:59:29 GMT

←Older revision		Revision as of 02:59, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PQI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PQI FirstGlance]. <br>
-	</td></tr><tr><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=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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi 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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi 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 36:		Line 38:
	[[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 19:43, 28 September 2014

OCA — Sun, 28 Sep 2014 19:43:26 GMT

←Older revision		Revision as of 19:43, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pqi.~~png~~\|~~left~~\|200px]]	+	==T4 LYSOZYME CORE REPACKING MUTANT I118L/CORE7/TA==
		+	<StructureSection load='1pqi' size='340' side='right' caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PQI FirstGlance]. <br>
		+	</td></tr><tr><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=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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [http://www.ebi.ac.uk/pdbsum/1pqi 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/pq/1pqi_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_1pqi\| PDB=1pqi \| 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 I118L~~/~~CORE7/TA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12963380}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1pqi]] 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=1PQI 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 11:53, 20 October 2012

OCA — Sat, 20 Oct 2012 11:53:35 GMT

←Older revision		Revision as of 11:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1pqi]] 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=1PQI OCA].	+	[[1pqi]] 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=1PQI OCA].

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

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

OCA — Thu, 26 Jul 2012 06:56:35 GMT

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

←Older revision

Revision as of 06:56, 26 July 2012

←Older revision		Revision as of 15:16, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1pqi' size='340' side='right'caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='1pqi' size='340' side='right'caption='[[1pqi]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pqi]] 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=1PQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQI FirstGlance]. <br>
	</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=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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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"><div style='overflow: auto; max-height: 3em;'>[[1p2l\|1p2l]], [[1p2r\|1p2r]], [[1p36\|1p36]], [[1p37\|1p37]], [[1p3n\|1p3n]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</div></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]], [[1p64\|1p64]], [[1p6y\|1p6y]], [[1p7s\|1p7s]], [[1pqd\|1pqd]], [[1pqj\|1pqj]], [[1pqm\|1pqm]], [[1pqo\|1pqo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">E ([https://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'>[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~~://proteopedia.org/fgij/fg.htm?mol=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [~~http~~://pdbe.org/1pqi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi 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=1pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqi OCA], [https://pdbe.org/1pqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pqi RCSB], [https://www.ebi.ac.uk/pdbsum/1pqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqi 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]]