1ji5: Difference between revisions

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 ==Dlp-1 from bacillus anthracis==
-<StructureSection load='1ji5' size='340' side='right' caption='[[1ji5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1ji5' size='340' side='right'caption='[[1ji5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ji5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ji5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JI5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ji4|1ji4]], [[1qgh|1qgh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dlp-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 Bacillus anthracis])</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=1ji5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji5 OCA], [https://pdbe.org/1ji5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ji5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ji5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji5 ProSAT]</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=1ji5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ji5 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji5 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPS2_BACAN DPS2_BACAN] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). It is capable of binding and sequestering Fe(2+) ion. Does not bind DNA.
 == 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/ji/1ji5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1ji5_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=1ji5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Bacillus anthracis is currently under intense investigation due to its primary importance as a human pathogen. Particularly important is the development of novel anti-anthrax vaccines, devoid of the current side effects. A novel class of immunogenic bacterial proteins consists of dodecamers homologous to the DNA-binding protein of Escherichia coli (Dps). Two Dps homologous genes are present in the B. anthracis genome. The crystal structures of these two proteins (Dlp-1 and Dlp-2) have been determined and are presented here. They are sphere-like proteins with an internal cavity. We also show that they act as ferritins and are thus involved in iron uptake and regulation, a fundamental function during bacterial growth.
-Structure of two iron-binding proteins from Bacillus anthracis.,Papinutto E, Dundon WG, Pitulis N, Battistutta R, Montecucco C, Zanotti G J Biol Chem. 2002 Apr 26;277(17):15093-8. Epub 2002 Feb 8. PMID:11836250<ref>PMID:11836250</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Bacillus anthracis]]
-[[Category: Battistutta, R]]
+[[Category: Large Structures]]
-[[Category: Dundon, W G]]
+[[Category: Battistutta R]]
-[[Category: Montecucco, C]]
+[[Category: Dundon WG]]
-[[Category: Papinutto, E]]
+[[Category: Montecucco C]]
-[[Category: Pitulis, N]]
+[[Category: Papinutto E]]
-[[Category: Zanotti, G]]
+[[Category: Pitulis N]]
-[[Category: Dodecamer]]
+[[Category: Zanotti G]]
-[[Category: Four-helix bundle]]
-[[Category: Metal transport]]