3dmz - Revision history

OCA at 12:50, 30 August 2023

OCA — Wed, 30 Aug 2023 12:50:02 GMT

←Older revision		Revision as of 12:50, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3dmz' size='340' side='right'caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3dmz' size='340' side='right'caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=HED:~~2~~-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [https://pdbe.org/3dmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [https://www.ebi.ac.uk/pdbsum/3dmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmz 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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [https://pdbe.org/3dmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [https://www.ebi.ac.uk/pdbsum/3dmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmz 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: Liu L]]
-	[[Category: Liu, L]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W]]~~	+
-	~~[[Category: Antimicrobial]]~~	+
-	~~[[Category: Bacteriolytic enzyme]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Halogen bond]]~~	+
-	~~[[Category: Halogenated benzene]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrophobic cavity]]~~	+
-	~~[[Category: T4 lysozyme~~]]	+

OCA at 19:25, 20 October 2021

OCA — Wed, 20 Oct 2021 19:25:23 GMT

←Older revision		Revision as of 19:25, 20 October 2021
Line 1:		Line 1:

	==Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant==		==Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant==
-	<StructureSection load='3dmz' size='340' side='right' caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3dmz' size='340' side='right'caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [~~http~~://pdbe.org/3dmz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dmz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmz 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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [https://pdbe.org/3dmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [https://www.ebi.ac.uk/pdbsum/3dmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmz 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]]
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Liu, L]]		[[Category: Liu, L]]

OCA at 09:38, 14 November 2018

OCA — Wed, 14 Nov 2018 09:38:02 GMT

←Older revision		Revision as of 09:38, 14 November 2018
Line 1:		Line 1:
		+
	==Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant==		==Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant==
	<StructureSection load='3dmz' size='340' side='right' caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3dmz' size='340' side='right' caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' 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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://pdbe.org/3dmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz 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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://pdbe.org/3dmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmz 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/dm/3dmz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/3dmz_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>

OCA at 06:59, 7 February 2016

OCA — Sun, 07 Feb 2016 06:59:50 GMT

←Older revision		Revision as of 06:59, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3dmz' size='340' side='right' caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3dmz' size='340' side='right' caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz 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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://pdbe.org/3dmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3dmz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3dmz" 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: Liu, L]]		[[Category: Liu, L]]

OCA at 08:49, 24 December 2014

OCA — Wed, 24 Dec 2014 08:49:02 GMT

←Older revision		Revision as of 08:49, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz 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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz 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: Liu, L.]]	+	[[Category: Liu, L]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]

OCA at 12:26, 29 September 2014

OCA — Mon, 29 Sep 2014 12:26:31 GMT

←Older revision		Revision as of 12:26, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3dmz.~~png~~\|~~left~~\|200px]]	+	==Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant==
		+	<StructureSection load='3dmz' size='340' side='right' caption='[[3dmz]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dmz]] 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=3DMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=HFB:HEXAFLUOROBENZENE'>HFB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[181l\|181l]], [[3dke\|3dke]], [[3dmv\|3dmv]], [[3dmx\|3dmx]], [[3dn0\|3dn0]], [[3dn1\|3dn1]], [[3dn2\|3dn2]], [[3dn3\|3dn3]], [[3dn4\|3dn4]], [[3dn6\|3dn6]], [[3dn8\|3dn8]], [[3dna\|3dna]]</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=3dmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dmz RCSB], [http://www.ebi.ac.uk/pdbsum/3dmz 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/dm/3dmz_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 ==
		+	We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume approximately 150 A(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystallography and related techniques to analyze the binding of halogen-incorporated benzenes typified by C(6)F(5)X, where X=H, F, Cl, Br or I, and C(6)H(5)X, where X=H or I was also studied. Because of the increased electron density of fluorine relative to hydrogen, the geometry of binding of the fluoro compounds can often be determined more precisely than their hydrogen-containing analogs. All of the ligands bind in essentially the same plane but the center of the phenyl ring can translate by up to 1.2 A. In no case does the ligand rotate freely within the cavity. The walls of the cavity consist predominantly of hydrocarbon atoms, and in several cases it appears that van der Waals interactions define the geometry of binding. In comparing the smallest with the largest ligand, the cavity volume increases from 181 A(3) to 245 A(3). This shows that the protein is flexible and adapts to the size and shape of the ligand. There is a remarkably close contact of 3.0 A between the iodine atom on C(6)F(5)I and the sulfur or selenium atom of Met or SeMet102. This interaction is 1.0 A less than the sum of the van der Waals radii and is a clear example of a so-called halogen bond. Notwithstanding this close approach, the increase in binding energy for the halogen bond relative to a van der Waals contact is estimated to be only about 0.5-0.7 kcal/mol.

-	~~{{STRUCTURE_3dmz\| PDB=3dmz \| SCENE= }}~~	+	Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding.,Liu L, Baase WA, Matthews BW J Mol Biol. 2009 Jan 16;385(2):595-605. Epub 2008 Nov 6. PMID:19014950<ref>PMID:19014950</ref>

-	~~===Hexafluorobenzene binding in~~ the ~~hydrophobic cavity of T4 lysozyme L99A mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19014950}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3dmz]] 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=3DMZ 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:019014950<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 05:55, 20 October 2012

OCA — Sat, 20 Oct 2012 05:55:25 GMT

←Older revision		Revision as of 05:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3dmz]] 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=3DMZ OCA].	+	[[3dmz]] 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=3DMZ OCA].

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

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

OCA — Wed, 25 Jul 2012 11:33:20 GMT

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

←Older revision

Revision as of 11:33, 25 July 2012

OCA at 11:33, 25 July 2012

OCA — Wed, 25 Jul 2012 11:33:18 GMT

←Older revision		Revision as of 11:33, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3dmz.png\|left\|200px]]		[[Image:3dmz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dmz", 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_3dmz\| PDB=3dmz \| SCENE= }}		{{STRUCTURE_3dmz\| PDB=3dmz \| SCENE= }}

	===Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant===		===Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19014950}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19014950 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19014950}}		{{ABSTRACT_PUBMED_19014950}}

	==About this Structure==		==About this Structure==
-	~~3DMZ~~ 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=3DMZ OCA].	+	[[3dmz]] 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=3DMZ OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19014950~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019014950</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
Line 36:		Line 27:
	[[Category: Hydrophobic cavity]]		[[Category: Hydrophobic cavity]]
	[[Category: T4 lysozyme]]		[[Category: T4 lysozyme]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:07:23 2009''

OCA at 10:07, 16 February 2009

OCA — Mon, 16 Feb 2009 10:07:25 GMT

←Older revision		Revision as of 10:07, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3DMZ is a ~~[[Single protein]]~~ 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=3DMZ OCA].	+	3DMZ 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=3DMZ OCA].

	==Reference==		==Reference==
-	Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding., Liu L, Baase WA, Matthews BW, J Mol Biol. 2009 Jan 16;385(2):595-605. Epub 2008 Nov 6. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19014950 19014950]~~	+	<ref group="xtra">PMID:19014950</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Liu, L.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx:audit_author~~.]]	+	[[Category: Matthews, B W.]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]
Line 37:		Line 37:
	[[Category: T4 lysozyme]]		[[Category: T4 lysozyme]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jan 28 20~~:33:16 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:07:23 2009''