6agg: Difference between revisions

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 ==Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)==
-<StructureSection load='6agg' size='340' side='right' caption='[[6agg]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
+<StructureSection load='6agg' size='340' side='right'caption='[[6agg]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6agg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AGG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6agg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AGG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.706&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xob|5xob]]</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=6agg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agg OCA], [https://pdbe.org/6agg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6agg RCSB], [https://www.ebi.ac.uk/pdbsum/6agg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6agg ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tiaS, AF_2259 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA(Ile)(2)-agmatinylcytidine_synthase tRNA(Ile)(2)-agmatinylcytidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.22 6.3.4.22] </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=6agg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agg OCA], [http://pdbe.org/6agg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agg RCSB], [http://www.ebi.ac.uk/pdbsum/6agg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TIAS_ARCFU TIAS_ARCFU]] ATP-dependent agmatine transferase that catalyzes the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2), converting the codon specificity from AUG to AUA.<ref>PMID:20139989</ref>
+[https://www.uniprot.org/uniprot/TIAS_ARCFU TIAS_ARCFU] ATP-dependent agmatine transferase that catalyzes the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2), converting the codon specificity from AUG to AUA.<ref>PMID:20139989</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
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 __TOC__
 </StructureSection>
-[[Category: Arcfu]]
+[[Category: Archaeoglobus fulgidus DSM 4304]]
-[[Category: Dong, J S]]
+[[Category: Large Structures]]
-[[Category: Gong, W M]]
+[[Category: Dong JS]]
-[[Category: Conformational change]]
+[[Category: Gong WM]]
-[[Category: Ligase]]
-[[Category: Tia]]
-[[Category: Trna modification]]
-[[Category: Zinc finger engineering]]
-[[Category: Zinc ribbon]]