1xpp: Difference between revisions

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 ==Crystal Structure of TA1416,DNA-directed RNA polymerase subunit L, from Thermoplasma acidophilum==
-<StructureSection load='1xpp' size='340' side='right' caption='[[1xpp]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='1xpp' size='340' side='right'caption='[[1xpp]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XPP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xpp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XPP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 1.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=1xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xpp OCA], [https://pdbe.org/1xpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xpp RCSB], [https://www.ebi.ac.uk/pdbsum/1xpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xpp ProSAT], [https://www.topsan.org/Proteins/MCSG/1xpp TOPSAN]</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=1xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xpp RCSB], [http://www.ebi.ac.uk/pdbsum/1xpp PDBsum], [http://www.topsan.org/Proteins/MCSG/1xpp TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOL_THEAC RPOL_THEAC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).
+[https://www.uniprot.org/uniprot/RPO11_THEAC RPO11_THEAC] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00261]
 == 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/xp/1xpp_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xp/1xpp_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=1xpp ConSurf].
 <div style="clear:both"></div>
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 __TOC__
 </StructureSection>
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Thermoplasma acidophilum]]
-[[Category: Edwards, A]]
+[[Category: Edwards A]]
-[[Category: Evdokimova, E]]
+[[Category: Evdokimova E]]
-[[Category: Joachimiak, A]]
+[[Category: Joachimiak A]]
-[[Category: Kim, Y]]
+[[Category: Kim Y]]
-[[Category: Structural genomic]]
+[[Category: Savchenko A]]
-[[Category: Savchenko, A]]
-[[Category: Dna-directed rna polymerase]]
-[[Category: Mcsg]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Transferase]]