2olc: Difference between revisions

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-{{Seed}}
-[[Image:2olc.png|left|200px]]
-<!--
+==Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho==
-The line below this paragraph, containing "STRUCTURE_2olc", creates the "Structure Box" on the page.
+<StructureSection load='2olc' size='340' side='right'caption='[[2olc]], [[Resolution|resolution]] 2.00&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'>[[2olc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OLC 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=HO:HOLMIUM+ATOM'>HO</scene></td></tr>
-{{STRUCTURE_2olc|  PDB=2olc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2olc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2olc OCA], [https://pdbe.org/2olc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2olc RCSB], [https://www.ebi.ac.uk/pdbsum/2olc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2olc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MTNK_BACSU MTNK_BACSU] Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate.<ref>PMID:11545674</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/ol/2olc_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=2olc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Trivalent holmium ions were shown to isomorphously replace magnesium ions to form an ADP-2Ho complex in the nucleotide-binding domain of Bacillus subtilis 5-methylthioribose (MTR) kinase. This nucleotide-holmium complex provided sufficient phasing power to allow SAD and SIRAS phasing of this previously unknown structure using the L(III) absorption edge of holmium. The structure of ADP-2Ho reveals that the two Ho ions are approximately 4 A apart and are likely to share their ligands: the phosphoryl O atoms of ADP and a water molecule. The structure determination of MTR kinase using data collected using Cu Kalpha X-radiation was also attempted. Although the heavy-atom substructure determination was successful, interpretation of the map was more challenging. The isomorphous substitution of holmium for magnesium in the MTR kinase-nucleotide complex suggests that this could be a useful phasing tool for other metal-dependent nucleotide-containing proteins.
-===Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho===
+ADP-2Ho as a phasing tool for nucleotide-containing proteins.,Ku SY, Smith GD, Howell PL Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):493-9. Epub 2007, Mar 16. PMID:17372354<ref>PMID:17372354</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17372354}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2olc" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17372354 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17372354}}
+__TOC__
+</StructureSection>
-==About this Structure==
-OLC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLC OCA].
-==Reference==
-ADP-2Ho as a phasing tool for nucleotide-containing proteins., Ku SY, Smith GD, Howell PL, Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):493-9. Epub 2007, Mar 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17372354 17372354]
 [[Category: Bacillus subtilis]]
-[[Category: S-methyl-5-thioribose kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Howell PL]]
-[[Category: Howell, P L.]]
+[[Category: Ku SY]]
-[[Category: Ku, S Y.]]
+[[Category: Smith GD]]
-[[Category: Smith, G D.]]
-[[Category: Kinase adp-2ho complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:47:09 2008''