1d3f: Difference between revisions

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-[[Image:1d3f.jpg|left|200px]]
-<!--
+==N-TERMINAL DOMAIN CORE METHIONINE MUTATION==
-The line below this paragraph, containing "STRUCTURE_1d3f", creates the "Structure Box" on the page.
+<StructureSection load='1d3f' size='340' side='right'caption='[[1d3f]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1d3f]] 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=1D3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3F FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</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></td></tr>
-{{STRUCTURE_1d3f|  PDB=1d3f  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3f OCA], [https://pdbe.org/1d3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3f RCSB], [https://www.ebi.ac.uk/pdbsum/1d3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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/d3/1d3f_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/main_output.php?pdb_ID=1d3f ConSurf].
+<div style="clear:both"></div>
-'''N-TERMINAL DOMAIN CORE METHIONINE MUTATION'''
+==See Also==
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Overview==
+<references/>
-Using heavily methionine-substituted T4 lysozyme as an example, it is shown how the addition or deletion of a small number of methionines can simplify the location of selenium sites for use in MAD phasing. By comparing the X-ray data for a large number of singly substituted lysozymes, it is shown that the optimal amino acid to be substituted by methionine is leucine, followed, in order of preference, by phenylalanine, isoleucine and valine. The identification of leucine as the first choice agrees with the ranking suggested by the Dayhoff mutation probability, i.e. by the frequency of amino-acid substitutions in the sequences of related proteins. The ranking of the second and subsequent choices, however, differ significantly.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-D3F 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=1D3F OCA].
+[[Category: Large Structures]]
+[[Category: Gassner NC]]
-==Reference==
+[[Category: Matthews BW]]
-Use of differentially substituted selenomethionine proteins in X-ray structure determination., Gassner NC, Matthews BW, Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1967-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10666571 10666571]
-[[Category: Enterobacteria phage t4]]
-[[Category: Lysozyme]]
-[[Category: Single protein]]
-[[Category: Gassner, N C.]]
-[[Category: Matthews, B W.]]
-[[Category: Methionine core mutant]]
-[[Category: Protein engineering]]
-[[Category: Protein folding]]
-[[Category: T4 lysozyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:24:28 2008''