173l: Difference between revisions

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 ==PROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF T4 LYSOZYME==
-<StructureSection load='173l' size='340' side='right' caption='[[173l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='173l' size='340' side='right'caption='[[173l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[173l]] 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=173L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=173L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[173l]] 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=173L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=173L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></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]] 1.7&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></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=173l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=173l OCA], [http://pdbe.org/173l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=173l RCSB], [http://www.ebi.ac.uk/pdbsum/173l PDBsum]</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=173l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=173l OCA], [https://pdbe.org/173l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=173l RCSB], [https://www.ebi.ac.uk/pdbsum/173l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=173l ProSAT]</span></td></tr>
 </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.
+[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 ==
 [[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/73/173l_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/73/173l_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].
+</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=173l ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structures of various mutants of T4 lysozyme have been determined in 25 non-isomorphous crystal forms. This provides an unusually diverse data base to compare the structures and dynamics of a closely related set of proteins in different crystal packing environments. In general, the more tightly packed crystals diffract better than those that are highly hydrated although the wild-type crystal form is an exception. The ability of the protein to form a relatively open but stable lattice may help explain why many of the mutants crystallize in this form. In different crystalline environments, the lysozyme molecules associate with 2-fold, 3-fold, 4-fold, and 5-fold symmetry, as well as with various types of screw associations. A "back-to-back" dimeric association, and a "head-to-tail" 2(1) screw association, are especially common, each occurring in more than half a dozen crystal forms. The 4-fold and 5-fold modes of association are closely related and provide an example of quasi-equivalent association as envisaged by Caspar and Klug. In different crystal environments the lysozyme molecules display a range of over 50 degrees in the hinge-bending angle between the amino and carboxy-terminal domains. Large variations in the hinge-bending angle are observed not only for lysozymes with mutations in the hinge region, but for molecules with mutations far from this site. This suggests that hinge-bending is an intrinsic property of the lysozyme molecule and is not an artifact due to mutation. As the hinge-bending angle increases about 15 degrees beyond that seen in wild-type there is a distinct conformations change in the side-chains of five residues in the hinge-bending region. Changes in the backbone are localized near residues 13, 59 and 80, but do not include significant changes in (phi, psi). Comparison of the different structures indicates that crystal contacts perturb the backbone structure of the protein by 0.2 to 0.5 A. These perturbations are of the same magnitude for helices and beta-sheet strands, suggesting that protein structures can be defined and maintained equally well by hydrogen-bonding (i.e. strand-strand) or by non-hydrogen-bonding (i.e. helix-helix) interactions. The discrepancies between the lysozyme structures in different crystallographic environments are in line with other comparisons of independently determined protein crystal structures. They suggest that protein structures in general are subject to low energy changes in conformation of 0.2 to 0.5 A.(ABSTRACT TRUNCATED AT 400 WORDS)
-Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme.,Zhang XJ, Wozniak JA, Matthews BW J Mol Biol. 1995 Jul 21;250(4):527-52. PMID:7616572<ref>PMID:7616572</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 173l" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Bpt4]]
+[[Category: Escherichia virus T4]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Matthews, B W]]
+[[Category: Matthews BW]]
-[[Category: Sun, D]]
+[[Category: Sun D]]
-[[Category: Xiong, X P]]
+[[Category: Xiong X-P]]
-[[Category: Zhang, X J]]
+[[Category: Zhang X-J]]