1qth - Revision history

OCA at 08:17, 14 February 2024

OCA — Wed, 14 Feb 2024 08:17:32 GMT

←Older revision		Revision as of 08:17, 14 February 2024
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	<StructureSection load='1qth' size='340' side='right'caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1qth' size='340' side='right'caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QTH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QTH FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[1qsb\|1qsb]]~~, [[~~1qs5~~\|~~1qs5~~]]~~, [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</div></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]] 1.9Å</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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [https://pdbe.org/1qth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [https://www.ebi.ac.uk/pdbsum/1qth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qth 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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [https://pdbe.org/1qth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [https://www.ebi.ac.uk/pdbsum/1qth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qth ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~LYS_BPT4 LYS_BPT4~~]~~] Helps~~ to ~~release~~ the mature ~~phage~~ particles ~~from~~ the cell ~~wall by breaking~~ down the peptidoglycan.	+	[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1qth 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=1qth ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In order to try to better understand the role played by strain in the structure and stability of a protein a series of "small-to-large" mutations was made within the core of T4 lysozyme. Three different alanine residues, one involved in backbone contacts, one in side-chain contacts, and the third adjacent to a small cavity, were each replaced with subsets of the larger residues, Val, Leu, Ile, Met, Phe and Trp. As expected, the protein is progressively destabilized as the size of the introduced side-chain becomes larger. There does, however, seem to be a limit to the destabilization, suggesting that a protein of a given size may be capable of maintaining only a certain amount of strain. The changes in stability vary greatly from site to site. Substitution of larger residues for both Ala42 and Ala98 substantially destabilize the protein, even though the primary contacts in one case are predominantly with side-chain atoms and in the other with backbone. The results suggest that it is neither practical nor meaningful to try to separate the effects of introduced strain on side-chains from the effects on the backbone. Substitutions at Ala129 are much less destabilizing than at sites 42 or 98. This is most easily understood in terms of the pre-existing cavity, which provides partial space to accommodate the introduced side-chains. Crystal structures were obtained for a number of the mutants. These show that the changes in structure to accommodate the introduced side-chains usually consist of essentially rigid-body displacements of groups of linked atoms, achieved through relatively small changes in torsion angles. On rare occasions, a side-chain close to the site of substitution may change to a different rotamer. When such rotomer changes occur, they permit the structure to dissipate strain by a response that is plastic rather than elastic. In one case, a surface loop moves 1.2 A, not in direct response to a mutation, but in an interaction mediated via an intermolecular contact. It illustrates how the structure of a protein can be modified by crystal contacts.
-
-	The introduction of strain and its effects on the structure and stability of T4 lysozyme.,Liu R, Baase WA, Matthews BW J Mol Biol. 2000 Jan 7;295(1):127-45. PMID:10623513<ref>PMID:10623513</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qth" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Baase WA]]
-	[[Category: Baase~~, W A~~]]	+	[[Category: Liu R]]
-	[[Category: Liu, R]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Stability]]~~	+
-	~~[[Category: Strain]]~~	+
-	~~[[Category: T4 lysozyme~~]]	+

OCA at 10:03, 15 September 2021

OCA — Wed, 15 Sep 2021 10:03:52 GMT

←Older revision		Revision as of 10:03, 15 September 2021
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	<StructureSection load='1qth' size='340' side='right'caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1qth' size='340' side='right'caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QTH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QTH FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [~~http~~://pdbe.org/1qth PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qth PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qth 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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [https://pdbe.org/1qth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [https://www.ebi.ac.uk/pdbsum/1qth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qth 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]]

OCA at 11:53, 4 December 2019

OCA — Wed, 04 Dec 2019 11:53:47 GMT

←Older revision		Revision as of 11:53, 4 December 2019
Line 1:		Line 1:

	==THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME==		==THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME==
-	<StructureSection load='1qth' size='340' side='right' caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1qth' size='340' side='right'caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 08:17, 28 February 2018

OCA — Wed, 28 Feb 2018 08:17:41 GMT

←Older revision		Revision as of 08:17, 28 February 2018
Line 1:		Line 1:
		+
	==THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME==		==THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME==
	<StructureSection load='1qth' size='340' side='right' caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1qth' size='340' side='right' caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://pdbe.org/1qth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth 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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://pdbe.org/1qth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qth ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/qt/1qth_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qt/1qth_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 10:01, 7 February 2016

OCA — Sun, 07 Feb 2016 10:01:24 GMT

←Older revision		Revision as of 10:01, 7 February 2016
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	<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=1qth ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:23, 10 September 2015

OCA — Thu, 10 Sep 2015 00:23:52 GMT

←Older revision		Revision as of 00:23, 10 September 2015
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	<StructureSection load='1qth' size='340' side='right' caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1qth' size='340' side='right' caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth 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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://pdbe.org/1qth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1qth" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baase, W A]]		[[Category: Baase, W A]]

OCA at 14:16, 24 December 2014

OCA — Wed, 24 Dec 2014 14:16:19 GMT

←Older revision		Revision as of 14:16, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth 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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth 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 34:		Line 36:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Baase, W A.]]	+	[[Category: Baase, W A]]
-	[[Category: Liu, R.]]	+	[[Category: Liu, R]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mutant]]		[[Category: Mutant]]

OCA at 22:09, 28 September 2014

OCA — Sun, 28 Sep 2014 22:09:55 GMT

←Older revision		Revision as of 22:09, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1qth.~~png~~\|~~left~~\|200px]]	+	==THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME==
		+	<StructureSection load='1qth' size='340' side='right' caption='[[1qth]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qth]] 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=1QTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QTH FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qsb\|1qsb]], [[1qs5\|1qs5]], [[1qs9\|1qs9]], [[1qtb\|1qtb]], [[1qtc\|1qtc]], [[1qtd\|1qtd]]</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=1qth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qth RCSB], [http://www.ebi.ac.uk/pdbsum/1qth 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/qt/1qth_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 ==
		+	In order to try to better understand the role played by strain in the structure and stability of a protein a series of "small-to-large" mutations was made within the core of T4 lysozyme. Three different alanine residues, one involved in backbone contacts, one in side-chain contacts, and the third adjacent to a small cavity, were each replaced with subsets of the larger residues, Val, Leu, Ile, Met, Phe and Trp. As expected, the protein is progressively destabilized as the size of the introduced side-chain becomes larger. There does, however, seem to be a limit to the destabilization, suggesting that a protein of a given size may be capable of maintaining only a certain amount of strain. The changes in stability vary greatly from site to site. Substitution of larger residues for both Ala42 and Ala98 substantially destabilize the protein, even though the primary contacts in one case are predominantly with side-chain atoms and in the other with backbone. The results suggest that it is neither practical nor meaningful to try to separate the effects of introduced strain on side-chains from the effects on the backbone. Substitutions at Ala129 are much less destabilizing than at sites 42 or 98. This is most easily understood in terms of the pre-existing cavity, which provides partial space to accommodate the introduced side-chains. Crystal structures were obtained for a number of the mutants. These show that the changes in structure to accommodate the introduced side-chains usually consist of essentially rigid-body displacements of groups of linked atoms, achieved through relatively small changes in torsion angles. On rare occasions, a side-chain close to the site of substitution may change to a different rotamer. When such rotomer changes occur, they permit the structure to dissipate strain by a response that is plastic rather than elastic. In one case, a surface loop moves 1.2 A, not in direct response to a mutation, but in an interaction mediated via an intermolecular contact. It illustrates how the structure of a protein can be modified by crystal contacts.

-	~~{{STRUCTURE_1qth\| PDB=1qth \| SCENE= }}~~	+	The introduction of strain and its effects on the structure and stability of T4 lysozyme.,Liu R, Baase WA, Matthews BW J Mol Biol. 2000 Jan 7;295(1):127-45. PMID:10623513<ref>PMID:10623513</ref>

-	~~===THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10623513}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1qth]] 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=1QTH 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:010623513<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 06:18, 20 October 2012

OCA — Sat, 20 Oct 2012 06:18:55 GMT

←Older revision		Revision as of 06:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1qth]] 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=1QTH OCA].	+	[[1qth]] 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=1QTH OCA].

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

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

OCA — Wed, 25 Jul 2012 12:47:20 GMT

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

←Older revision

Revision as of 12:47, 25 July 2012