2i5r: Difference between revisions

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 ==Structure of small Toprim domain-containing protein from B. stearothermophilus in complex with Mg2+==
-<StructureSection load='2i5r' size='340' side='right' caption='[[2i5r]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='2i5r' size='340' side='right'caption='[[2i5r]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2i5r]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I5R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2i5r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I5R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.65&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fcj|2fcj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2i5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i5r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i5r RCSB], [http://www.ebi.ac.uk/pdbsum/2i5r PDBsum], [http://www.topsan.org/Proteins/MCSG/2i5r TOPSAN]</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=2i5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i5r OCA], [https://pdbe.org/2i5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i5r RCSB], [https://www.ebi.ac.uk/pdbsum/2i5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i5r ProSAT], [https://www.topsan.org/Proteins/MCSG/2i5r TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5KVJ9_GEOKA Q5KVJ9_GEOKA]
 == 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/i5/2i5r_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/2i5r_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=2i5r ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of the Midwest Center for Structural Genomics target APC35832, a 14.7-kDa cytosolic protein from Bacillus stearothermophilus, has been determined at 1.3 A resolution by the single anomalous diffraction method from a mercury soaked crystal. The APC35832 protein is a representative of large group of bacterial and archeal proteins entirely consisting of the Toprim (topoisomerase-primase) domain. This domain is found in the catalytic centers of many enzymes catalyzing phosphodiester bond formation or cleavage, but the function of small Toprim domain proteins remains unknown. Consistent with the sequence analysis, the APC35832 structure shows a conserved Toprim fold, with a central 4-stranded parallel beta-sheet surrounded by four alpha-helixes. Comparison of the APC35832 structure with its closest structural homolog, the catalytic core of bacteriophage T7 primase, revealed structural conservation of a metal binding site and isothermal titration calorimetry indicates that APC35832 binds Mg2+ with a sub-millimolar dissociation constant (K(d)). The APC35832-Mg2+ complex structure was determined at 1.65 A and reveals the role of conserved acidic residues in Mg2+ ion coordination. The structural similarities to other Toprim domain containing proteins and potential function and substrates of APC35832 are discussed in this article.
-Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus.,Rezacova P, Borek D, Moy SF, Joachimiak A, Otwinowski Z Proteins. 2008 Feb 1;70(2):311-9. PMID:17705269<ref>PMID:17705269</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
 *[[TOPRIM domain protein|TOPRIM domain protein]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Borek, D]]
+[[Category: Large Structures]]
-[[Category: Joachimiak, A]]
+[[Category: Borek D]]
-[[Category: Structural genomic]]
+[[Category: Joachimiak A]]
-[[Category: Moy, S F]]
+[[Category: Moy SF]]
-[[Category: Otwinowski, Z]]
+[[Category: Otwinowski Z]]
-[[Category: Rezacova, P]]
+[[Category: Rezacova P]]
-[[Category: Mcsg]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Toprim domain]]
-[[Category: Unknown function]]