2d4j - Revision history

OCA at 08:24, 25 October 2023

OCA — Wed, 25 Oct 2023 08:24:14 GMT

←Older revision		Revision as of 08:24, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>~~, ~~<scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.16Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2d4i\|2d4i]], [[2d4k\|2d4k]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [https://pdbe.org/2d4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [https://www.ebi.ac.uk/pdbsum/2d4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4j 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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [https://pdbe.org/2d4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [https://www.ebi.ac.uk/pdbsum/2d4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>	+	[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 38:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Akiba T]]
-	[[Category: Akiba, T]]	+	[[Category: Harata K]]
-	[[Category: Harata, K]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phase transition]]~~	+
-	~~[[Category: Rigid-body motion]]~~	+
-	~~[[Category: Tls analysis~~]]	+

OCA at 20:37, 20 October 2021

OCA — Wed, 20 Oct 2021 20:37:33 GMT

←Older revision		Revision as of 20:37, 20 October 2021
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	<StructureSection load='2d4j' size='340' side='right'caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>		<StructureSection load='2d4j' size='340' side='right'caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d4i\|2d4i]], [[2d4k\|2d4k]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [~~http~~://pdbe.org/2d4j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d4j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4j 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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [https://pdbe.org/2d4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [https://www.ebi.ac.uk/pdbsum/2d4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>	+	[[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:40, 11 December 2019

OCA — Wed, 11 Dec 2019 19:40:55 GMT

←Older revision		Revision as of 19:40, 11 December 2019
Line 1:		Line 1:

	==Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution==		==Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution==
-	<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>	+	<StructureSection load='2d4j' size='340' side='right'caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2d4j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2d4j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Akiba, T]]		[[Category: Akiba, T]]

OCA at 18:48, 24 January 2018

OCA — Wed, 24 Jan 2018 18:48:10 GMT

←Older revision		Revision as of 18:48, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>		<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</td></tr>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/2d4j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/2d4j_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2d4j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2d4j" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chick~~]]	+	[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Akiba, T]]		[[Category: Akiba, T]]

OCA at 14:19, 12 October 2017

OCA — Thu, 12 Oct 2017 14:19:26 GMT

←Older revision		Revision as of 14:19, 12 October 2017
Line 1:		Line 1:
		+
	==Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution==		==Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution==
	<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>		<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://pdbe.org/2d4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j 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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://pdbe.org/2d4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 06:41, 8 February 2016

OCA — Mon, 08 Feb 2016 06:41:06 GMT

←Older revision		Revision as of 06:41, 8 February 2016
Line 18:		Line 18:
	<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=2d4j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:53, 10 September 2015

OCA — Thu, 10 Sep 2015 08:53:49 GMT

←Older revision		Revision as of 08:53, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>		<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Gallus_gallus Gallus gallus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j 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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://pdbe.org/2d4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2d4j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Chick]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Akiba, T]]		[[Category: Akiba, T]]

OCA at 21:22, 24 December 2014

OCA — Wed, 24 Dec 2014 21:22:25 GMT

←Older revision		Revision as of 21:22, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j 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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Akiba, T.]]	+	[[Category: Akiba, T]]
-	[[Category: Harata, K.]]	+	[[Category: Harata, K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phase transition]]		[[Category: Phase transition]]
	[[Category: Rigid-body motion]]		[[Category: Rigid-body motion]]
	[[Category: Tls analysis]]		[[Category: Tls analysis]]

OCA at 05:55, 29 September 2014

OCA — Mon, 29 Sep 2014 05:55:43 GMT

←Older revision		Revision as of 05:55, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2d4j.~~png~~\|~~left~~\|200px]]	+	==Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution==
		+	<StructureSection load='2d4j' size='340' side='right' caption='[[2d4j]], [[Resolution\|resolution]] 1.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d4i\|2d4i]], [[2d4k\|2d4k]]</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=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [http://www.ebi.ac.uk/pdbsum/2d4j 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/d4/2d4j_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 ==
		+	Two monoclinic crystals (space group P2(1)) of hen egg-white lysozyme, a type I crystal grown at room temperature in a D2O solution with pD 4.5 containing 2%(w/v) sodium nitrate and a type II crystal grown at 313 K in a 10%(w/v) sodium chloride solution with pH 7.6, were each transformed into another monoclinic crystal with the same space group by dehydration-induced phase transition. Changes in X-ray diffraction were recorded to monitor the progress of the crystal transformation, which started with the appearance of diffuse streaks. In both crystals, the intensity of h + l odd reflections gradually weakened and finally disappeared on completion of the transformation. X-ray diffraction in the intermediate state indicated the presence of lattices of both the native and transformed crystals. In the native type I crystal, two alternate conformations were observed in the main chain of the region Gly71-Asn74. One conformer bound a sodium ion which was replaced with a water molecule in the other conformer. In the transformed crystal, the sodium ion was removed and the main-chain conformation of this region was converted to that of the water-bound form. The transformed crystal diffracted to a higher resolution than the native crystal, while the peak width of the diffraction spots increased. Analysis of the thermal motion of protein molecules using the TLS model has shown that the enhancement of the diffraction power in the transformed crystal is mainly ascribable to the suppression of rigid-body motion owing to an increase in intermolecular contacts as a result of the loss of bulk solvent.

-	~~{{STRUCTURE_2d4j\| PDB=2d4j \| SCENE= }}~~	+	Structural phase transition of monoclinic crystals of hen egg-white lysozyme.,Harata K, Akiba T Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):375-82. Epub 2006, Mar 18. PMID:16552138<ref>PMID:16552138</ref>

-	~~===Transformed monoclinic crystal~~ of ~~hen egg-white lysozyme from a heavy water solution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16552138}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2d4j]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Gallus_gallus Gallus gallus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J 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:016552138<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 09:16, 20 October 2012

OCA — Sat, 20 Oct 2012 09:16:31 GMT

←Older revision		Revision as of 09:16, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2d4j]] is a 1 chain structure ~~of [[Hen Egg-White (HEW) Lysozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA].	+	[[2d4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA].

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