2dv3: Difference between revisions

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 ==Crystal structure of Leu65 to Arg mutant of Diphthine synthase==
-<StructureSection load='2dv3' size='340' side='right' caption='[[2dv3]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2dv3' size='340' side='right'caption='[[2dv3]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dv3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DV3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dv3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DV3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wng|1wng]], [[2dv4|2dv4]], [[2dv5|2dv5]], [[2dv7|2dv7]]</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dphB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=2dv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dv3 OCA], [https://pdbe.org/2dv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dv3 RCSB], [https://www.ebi.ac.uk/pdbsum/2dv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dv3 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dv3 TOPSAN]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphthine_synthase Diphthine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.98 2.1.1.98] </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=2dv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dv3 OCA], [http://pdbe.org/2dv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dv3 RCSB], [http://www.ebi.ac.uk/pdbsum/2dv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dv3 ProSAT], [http://www.topsan.org/Proteins/RSGI/2dv3 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPHB_PYRHO DPHB_PYRHO]] S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.<ref>PMID:20873788</ref>
+[https://www.uniprot.org/uniprot/DPHB_PYRHO DPHB_PYRHO] S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.<ref>PMID:20873788</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/dv/2dv3_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dv3_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Diphthine synthase]]
+[[Category: Large Structures]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Kunishima, N]]
+[[Category: Kunishima N]]
-[[Category: Matsuura, Y]]
+[[Category: Matsuura Y]]
-[[Category: Mizutani, H]]
+[[Category: Mizutani H]]
-[[Category: Structural genomic]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Rsgi]]
-[[Category: Transferase]]