3cdt: Difference between revisions

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 ==Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme==
-<StructureSection load='3cdt' size='340' side='right' caption='[[3cdt]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
+<StructureSection load='3cdt' size='340' side='right'caption='[[3cdt]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3cdt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CDT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3cdt]] 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=3CDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CDT 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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.63&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1l34|1l34]], [[1l63|1l63]], [[3c7w|3c7w]], [[3c7y|3c7y]], [[3c7z|3c7z]], [[3c80|3c80]], [[3c81|3c81]], [[3c82|3c82]], [[3c83|3c83]], [[3c8q|3c8q]], [[3c8r|3c8r]], [[3c8s|3c8s]], [[3cdo|3cdo]], [[3cdq|3cdq]], [[3cdr|3cdr]], [[3cdv|3cdv]], [[3f8v|3f8v]], [[3f9l|3f9l]], [[3fa0|3fa0]], [[3fad|3fad]], [[3fi5|3fi5]]</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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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= Bacteriophage T4])</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=3cdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdt OCA], [https://pdbe.org/3cdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cdt RCSB], [https://www.ebi.ac.uk/pdbsum/3cdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdt ProSAT]</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=3cdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdt OCA], [http://pdbe.org/3cdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cdt RCSB], [http://www.ebi.ac.uk/pdbsum/3cdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdt 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/cd/3cdt_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/3cdt_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage t4]]
+[[Category: Escherichia virus T4]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Mooers, B H.M]]
+[[Category: Mooers BHM]]
-[[Category: Antimicrobial]]
-[[Category: Bacteriolytic enzyme]]
-[[Category: Bacteriophage t4 lysozyme]]
-[[Category: Cation binding]]
-[[Category: Charge burial]]
-[[Category: Glycosidase]]
-[[Category: Helix dipole]]
-[[Category: Hydrogen bonding]]
-[[Category: Hydrolase]]
-[[Category: Mutational analysis]]
-[[Category: Protein crevice]]
-[[Category: Protein electrostatic]]
-[[Category: Protein engineerng]]
-[[Category: Protein stability]]
-[[Category: Protein structure]]
-[[Category: Steric strain]]
-[[Category: Temperature-sensitive mutant]]
-[[Category: Thermal stability]]
-[[Category: Viral lysozyme]]