3gup - Revision history

OCA at 07:12, 6 September 2023

OCA — Wed, 06 Sep 2023 07:12:43 GMT

←Older revision		Revision as of 07:12, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3gup' size='340' side='right'caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3gup' size='340' side='right'caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GUP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CME~~:~~S,S-(2-HYDROXYETHYL)THIOCYSTEINE~~'>~~CME~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;~~'>~~[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]~~</~~div~~><~~/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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [https://pdbe.org/3gup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [https://www.ebi.ac.uk/pdbsum/3gup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gup 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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [https://pdbe.org/3gup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [https://www.ebi.ac.uk/pdbsum/3gup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gup 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 39:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Liu L]]
-	[[Category: Liu, L]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W]]~~	+
-	~~[[Category: Antimicrobial]]~~	+
-	~~[[Category: Apolar cavity]]~~	+
-	~~[[Category: Bacteriolytic enzyme]]~~	+
-	~~[[Category: Buried charge]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ligand binding]]~~	+
-	~~[[Category: T4 lysozyme~~]]	+

OCA at 11:52, 13 October 2021

OCA — Wed, 13 Oct 2021 11:52:10 GMT

←Older revision		Revision as of 11:52, 13 October 2021
Line 1:		Line 1:

	==T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding==		==T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding==
-	<StructureSection load='3gup' size='340' side='right' caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='3gup' size='340' side='right'caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GUP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [~~http~~://pdbe.org/3gup PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gup PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gup 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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [https://pdbe.org/3gup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [https://www.ebi.ac.uk/pdbsum/3gup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gup 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/gu/3gup_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gu/3gup_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 40:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Liu, L]]		[[Category: Liu, L]]

OCA at 15:32, 5 August 2016

OCA — Fri, 05 Aug 2016 15:32:12 GMT

←Older revision		Revision as of 15:32, 5 August 2016
Line 1:		Line 1:
		+
	==T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding==		==T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding==
	<StructureSection load='3gup' size='340' side='right' caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3gup' size='340' side='right' caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GUP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [http://www.ebi.ac.uk/pdbsum/3gup 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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [http://pdbe.org/3gup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [http://www.ebi.ac.uk/pdbsum/3gup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gup ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	<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=3gup ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	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 3gup" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Liu, L]]		[[Category: Liu, L]]

OCA at 19:55, 25 December 2014

OCA — Thu, 25 Dec 2014 19:55:57 GMT

←Older revision		Revision as of 19:55, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GUP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [http://www.ebi.ac.uk/pdbsum/3gup 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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [http://www.ebi.ac.uk/pdbsum/3gup 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 37:		Line 39:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Liu, L.]]	+	[[Category: Liu, L]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Apolar cavity]]		[[Category: Apolar cavity]]

OCA at 13:37, 29 September 2014

OCA — Mon, 29 Sep 2014 13:37:54 GMT

←Older revision		Revision as of 13:37, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3gup.~~png~~\|~~left~~\|200px]]	+	==T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding==
		+	<StructureSection load='3gup' size='340' side='right' caption='[[3gup]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gup]] is a 2 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=3GUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GUP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0PY:PYRIDINE'>0PY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gui\|3gui]], [[3guj\|3guj]], [[3guk\|3guk]], [[3gul\|3gul]], [[3gum\|3gum]], [[3gun\|3gun]], [[3guo\|3guo]]</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=3gup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gup RCSB], [http://www.ebi.ac.uk/pdbsum/3gup 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/gu/3gup_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 ==
		+	Both large-to-small and non-polar-to-polar mutations in the hydrophobic core of T4 lysozyme cause significant loss in stability. By including supplementary stabilizing mutations we constructed a variant that combines the cavity-creating substitution Leu99 Ala with the buried charge mutant Met102 Glu. Crystal structure determination confirmed that this variant has a large cavity with the side-chain of Glu102 located within the cavity wall. The cavity includes a large disk-shaped region plus a bulge. The disk-like region is essentially non-polar, similar to L99A, while the Glu102 substituent is located in the vicinity of the bulge. Three ordered water molecules bind within this part of the cavity and appear to stabilize the conformation of Glu102. Glu102 has an estimated pKa of about 5.5-6.5, suggesting that it is at least partially charged in the crystal structure. The polar ligands pyridine, phenol and aniline bind within the cavity and crystal structures of the complexes show one or two water molecules to be retained. Non-polar ligands of appropriate shape can also bind in the cavity and in some cases exclude all three water molecules. This disrupts the hydrogen-bond network and causes the Glu102 side-chain to move away from the ligand by up to 0.8 A where it remains buried in a completely non-polar environment. Isothermal titration calorimetry revealed that the binding of these compounds stabilizes the protein by 4 6 kcal/mol. For both polar and non polar ligands the binding is enthalpically driven. Large negative changes in entropy adversely balance the binding of the polar ligands, whereas entropy has little effect on the non polar ligand binding.

-	~~{{STRUCTURE_3gup\| PDB=3gup \| SCENE= }}~~	+	Use of Stabilizing Mutations to Engineer a Charged Group within a Ligand-binding Hydrophobic Cavity in T4 Lysozyme.,Liu L, Baase WA, Michael M, Matthews BW Biochemistry. 2009 Aug 10. PMID:19663503<ref>PMID:19663503</ref>

-	~~===T4 lysozyme M102E~~/~~L99A mutant with buried charge in apolar cavity--pyridine binding===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19663503}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3gup]] is~~ a ~~2 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=3GUP 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:019663503<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 20:49, 20 October 2012

OCA — Sat, 20 Oct 2012 20:49:16 GMT

←Older revision		Revision as of 20:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3gup]] is a 2 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=3GUP OCA].	+	[[3gup]] is a 2 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=3GUP OCA].

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

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

OCA — Fri, 27 Jul 2012 11:43:57 GMT

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

←Older revision

Revision as of 11:43, 27 July 2012

OCA at 11:43, 27 July 2012

OCA — Fri, 27 Jul 2012 11:43:55 GMT

←Older revision		Revision as of 11:43, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3gup.png\|left\|200px]]		[[Image:3gup.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gup", 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_3gup\| PDB=3gup \| SCENE= }}		{{STRUCTURE_3gup\| PDB=3gup \| SCENE= }}

	===T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding===		===T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19663503}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19663503 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19663503}}		{{ABSTRACT_PUBMED_19663503}}

	==About this Structure==		==About this Structure==
-	~~3GUP~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=3GUP OCA].	+	[[3gup]] is a 2 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=3GUP OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19663503~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019663503</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 36:		Line 27:
	[[Category: Ligand binding]]		[[Category: Ligand binding]]
	[[Category: T4 lysozyme]]		[[Category: T4 lysozyme]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 19:26:41 2009''

OCA at 16:26, 21 September 2009

OCA — Mon, 21 Sep 2009 16:26:42 GMT

←Older revision		Revision as of 16:26, 21 September 2009
Line 12:		Line 12:
	===T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding===		===T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19663503}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19663503 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19663503}}

	==About this Structure==		==About this Structure==
Line 31:		Line 37:
	[[Category: T4 lysozyme]]		[[Category: T4 lysozyme]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 16:54:02 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 19:26:41 2009''

OCA at 13:54, 21 September 2009

OCA — Mon, 21 Sep 2009 13:54:03 GMT

←Older revision		Revision as of 13:54, 21 September 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3gup.png\|left\|200px]]

-	The ~~entry 3gup~~ is ~~ON HOLD~~ ~~until Sep 30 2010~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3gup", 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_3gup\| PDB=3gup \| SCENE= }}

-	~~Authors: Liu, L., Matthews, B.W.~~	+	===T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding===

-	Description: T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed May 6 09~~:40:00 2009''	+	==About this Structure==
		+	3GUP is a 2 chains structure of sequences 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=3GUP OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19663503</ref><references group="xtra"/>
		+	[[Category: Enterobacteria phage t4]]
		+	[[Category: Lysozyme]]
		+	[[Category: Liu, L.]]
		+	[[Category: Matthews, B W.]]
		+	[[Category: Antimicrobial]]
		+	[[Category: Apolar cavity]]
		+	[[Category: Bacteriolytic enzyme]]
		+	[[Category: Buried charge]]
		+	[[Category: Glycosidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Ligand binding]]
		+	[[Category: T4 lysozyme]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 16:54:02 2009''