3cdv - Revision history

OCA at 12:26, 30 August 2023

2023-08-30T12:26:26Z

← Older revision		Revision as of 12:26, 30 August 2023
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	<StructureSection load='3cdv' size='340' side='right'caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3cdv' size='340' side='right'caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cdv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacteriophage_t4 Bacteriophage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CDV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cdv]] 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=3CDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CDV 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></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]] 1.73Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; max-height: 3em;'>[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</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></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 Bacteriophage T4])</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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [https://pdbe.org/3cdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [https://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv 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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [https://pdbe.org/3cdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [https://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv 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]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacteriophage t4~~]]		[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Lysozyme]]~~		[[Category: Mooers BHM]]
	[[Category: Mooers~~, B H.M]]~~
	~~[[Category: Antimicrobial]]~~
	~~[[Category: Bacteriolytic enzyme]]~~
	~~[[Category: Bacteriophage t4 lysozyme]]~~
	~~[[Category: Cation binding]]~~
	~~[[Category: Charge burial]]~~
	~~[[Category: Glycosidase]]~~
	~~[[Category: Helix dipole]]~~
	~~[[Category: Hydrogen bonding]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Mutational analysis]]~~
	~~[[Category: Protein crevice]]~~
	~~[[Category: Protein electrostatic]]~~
	~~[[Category: Protein engineering]]~~
	~~[[Category: Protein stability]]~~
	~~[[Category: Protein structure]]~~
	~~[[Category: Steric strain]]~~
	~~[[Category: Temperature-sensitive mutant]]~~
	~~[[Category: Thermal stability]]~~
	~~[[Category: Viral lysozyme~~]]

OCA at 19:09, 20 October 2021

2021-10-20T19:09:39Z

← Older revision		Revision as of 19:09, 20 October 2021
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	==Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme==		==Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme==
	<StructureSection load='3cdv' size='340' side='right' caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3cdv' size='340' side='right'caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cdv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CDV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CDV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cdv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CDV 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</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 Bacteriophage T4])</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 Bacteriophage T4])</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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [~~http~~://pdbe.org/3cdv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv 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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [https://pdbe.org/3cdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [https://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv 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]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/3cdv_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/3cdv_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 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacteriophage t4]]		[[Category: Bacteriophage t4]]
			[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Mooers, B H.M]]		[[Category: Mooers, B H.M]]

OCA at 08:25, 25 October 2017

2017-10-25T08:25:14Z

← Older revision		Revision as of 08:25, 25 October 2017
Line 6:		Line 6:
	</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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</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= Bacteriophage 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 Bacteriophage T4])</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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://pdbe.org/3cdv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv 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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://pdbe.org/3cdv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv ProSAT]</span></td></tr>

OCA at 01:42, 5 August 2016

2016-08-05T01:42:31Z

← Older revision		Revision as of 01:42, 5 August 2016
Line 1:		Line 1:

	==Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme==		==Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme==
	<StructureSection load='3cdv' size='340' side='right' caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3cdv' size='340' side='right' caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cdv]] 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=3CDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CDV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cdv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CDV 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</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= Bacteriophage T4])</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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv 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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://pdbe.org/3cdv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3cdv 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:
	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 3cdv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Enterobacteria phage~~ t4]]		[[Category: Bacteriophage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Mooers, B H.M]]		[[Category: Mooers, B H.M]]

OCA at 14:47, 25 December 2014

2014-12-25T14:47:50Z

← Older revision		Revision as of 14:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cdv]] 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=3CDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CDV FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cdv]] 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=3CDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CDV 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><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></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv 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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv 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: Mooers, B H.M.]]		[[Category: Mooers, B H.M]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]

OCA at 09:49, 29 September 2014

2014-09-29T09:49:15Z

← Older revision		Revision as of 09:49, 29 September 2014
Line 1:		Line 1:
	[[Image:~~3cdv~~.~~png~~\|~~left~~\|~~200px~~]]		==Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme==
			<StructureSection load='3cdv' size='340' side='right' caption='[[3cdv]], [[Resolution\|resolution]] 1.73Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3cdv]] 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=3CDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CDV 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><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l34\|1l34]], [[1l63\|1l63]], [[3c7w\|3c7w]], [[3c7y\|3c7y]], [[3c7z\|3c7z]], [[3c80\|3c80]], [[3c81\|3c81]], [[3c82\|3c82]], [[3c83\|3c83]], [[3c8q\|3c8q]], [[3c8r\|3c8r]], [[3c8s\|3c8s]], [[3cdo\|3cdo]], [[3cdq\|3cdq]], [[3cdr\|3cdr]], [[3cdt\|3cdt]], [[3f8v\|3f8v]], [[3f9l\|3f9l]], [[3fa0\|3fa0]], [[3fad\|3fad]], [[3fi5\|3fi5]]</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=3cdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cdv RCSB], [http://www.ebi.ac.uk/pdbsum/3cdv 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/cd/3cdv_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 ==
			To try to resolve the loss of stability in the temperature-sensitive mutant of T4 lysozyme, Arg 96 --> His, all of the remaining 18 naturally occurring amino acids were substituted at site 96. Also, in response to suggestions that the charged residues Lys85 and Asp89, which are 5-8 A away, may have important effects, each of these amino acids was replaced with alanine. Crystal structures were determined for many of the variants. With the exception of the tryptophan and valine mutants R96W and R96V, the crystallographic analysis shows that the substituted side chain following the path of Arg96 in wildtype (WT). The melting temperatures of the variants decrease by up to approximately 16 degrees C with WT being most stable. There are two site 96 replacements, with lysine or glutamine, that leave the stability close to that of WT. The only element that the side chains of these residues have in common with the WT arginine is the set of three carbon atoms at the C(alpha), C(beta), and C(gamma) positions. Although each side chain is long and flexible with a polar group at the distal position, the details of the hydrogen bonding to the rest of the protein differ in each case. Also, the glutamine replacement lacks a positive charge. This shows that there is some adaptability in achieving full stabilization at this site. At the other extreme, to be maximally destabilizing a mutation at site 96 must not only eliminate favorable interactions but also introduce an unfavorable element such as steric strain or a hydrogen-bonding group that remains unsatisfied. Overall, the study highlights the essential need for atomic resolution site-specific structural information to understand and to predict the stability of mutant proteins. It can be very misleading to simply assume that conservative amino acid substitutions cause small changes in stability, whereas large stability changes are associated with nonconservative replacements.

	~~{{STRUCTURE_3cdv\| PDB=3cdv \| SCENE= }}~~		Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.,Mooers BH, Baase WA, Wray JW, Matthews BW Protein Sci. 2009 May;18(5):871-80. PMID:19384988<ref>PMID:19384988</ref>

	~~===Contributions~~ of ~~all 20 amino acids at site 96 to~~ the ~~stability and structure of T4 lysozyme===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19384988}}~~

	~~==About this Structure==~~
	~~[[3cdv]] 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=3CDV 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:019384988<~~/~~ref~~><~~ref group="xtra">PMID:019384984</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 17:59, 20 October 2012

2012-10-20T17:59:30Z

← Older revision		Revision as of 17:59, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[3cdv]] 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=3CDV OCA].		[[3cdv]] 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=3CDV OCA].

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

OCA at 02:39, 27 July 2012

2012-07-27T02:39:09Z

← Older revision		Revision as of 02:39, 27 July 2012
Line 1:		Line 1:
	[[Image:3cdv.png\|left\|200px]]		[[Image:3cdv.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3cdv", 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_3cdv\| PDB=3cdv \| SCENE= }}		{{STRUCTURE_3cdv\| PDB=3cdv \| SCENE= }}

	===Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme===		===Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19384988}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19384988 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19384988}}		{{ABSTRACT_PUBMED_19384988}}

	==About this Structure==		==About this Structure==
	[[3cdv]] 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=3CDV OCA].		[[3cdv]] 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=3CDV OCA].

			==See Also==
			*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19384988~~</ref><ref group="xtra">PMID:~~19384984~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019384988</ref><ref group="xtra">PMID:019384984</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA: Protected "3cdv" [edit=sysop:move=sysop]

2011-03-14T23:37:13Z

Protected "3cdv" [edit=sysop:move=sysop]

← Older revision	Revision as of 23:37, 14 March 2011
(No difference)

OCA at 23:37, 14 March 2011

2011-03-14T23:37:12Z

← Older revision		Revision as of 23:37, 14 March 2011
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:3cdv.png\|left\|200px]]		[[Image:3cdv.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
	~~3CDV~~ 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=3CDV OCA].		[[3cdv]] 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=3CDV OCA].

	==Reference==		==Reference==
Line 46:		Line 45:
	[[Category: Thermal stability]]		[[Category: Thermal stability]]
	[[Category: Viral lysozyme]]		[[Category: Viral lysozyme]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 09:19:37 2009''~~