1n1q: Difference between revisions

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OCA

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-[[Image:1n1q.jpg|left|200px]]<br /><applet load="1n1q" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1n1q, resolution 2.20&Aring;" />
-'''Crystal structure of a Dps protein from Bacillus brevis'''<br />
-==Overview==
+==Crystal structure of a Dps protein from Bacillus brevis==
-The crystallization of cellular components represents a unique survival, strategy for bacterial cells under stressed conditions. A highly ordered, layered structure is often formed in such a process, which may involve one, or more than one type of bio-macromolecules. The main advantage of, biocrystallization has been attributed to the fact that it is a physical, process and thus is independent of energy consumption. Dps is a protein, that crystallizes to form a multi-layered structure in starved cells in, order to protect DNA against oxidative damage and other detrimental, factors. The multi-layered crystal structure of a Dps protein from, Bacillus brevis has been revealed for the first time at atomic resolution, in the absence of DNA. Inspection of the structure provides the first, direct evidence for the existence of a di-nuclear ferroxidase center, which possesses unique features among all the di-iron proteins identified, so far. It constitutes the structural basis for the ferroxidase activity, of Dps in the crystalline state as well as in solution. This finding, proves that the enzymatic process of detoxification of metal ions, which, may cause severe oxidative damage to DNA, is the other important aspect of, the defense mechanism performed by Dps. In the multi-layered structure, Dps dodecamers are organized in a highly ordered manner. They adopt the, classic form of hexagonal packing in each layer of the structure. Such, arrangement results in reinforced structural features that would, facilitate the attraction and absorption of metal ions from the, environment. The highly ordered layered structure may provide an ideal, basis for the accommodation of DNA between the layers so that it can be, isolated and protected from harmful factors under stress conditions.
+<StructureSection load='1n1q' size='340' side='right'caption='[[1n1q]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1n1q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N1Q FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene></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=1n1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1q OCA], [https://pdbe.org/1n1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n1q RCSB], [https://www.ebi.ac.uk/pdbsum/1n1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1q ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPS_BREBE DPS_BREBE]
+== 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/n1/1n1q_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=1n1q ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-N1Q is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis] with FEO as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N1Q OCA].
+*[[Ferritin 3D structures|Ferritin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-The multi-layered structure of Dps with a novel di-nuclear ferroxidase center., Ren B, Tibbelin G, Kajino T, Asami O, Ladenstein R, J Mol Biol. 2003 Jun 6;329(3):467-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12767829 12767829]
 [[Category: Brevibacillus brevis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Asami, O.]]
+[[Category: Asami O]]
-[[Category: Kajino, T.]]
+[[Category: Kajino T]]
-[[Category: Ladenstein, R.]]
+[[Category: Ladenstein R]]
-[[Category: Ren, B.]]
+[[Category: Ren B]]
-[[Category: Tibbelin, G.]]
+[[Category: Tibbelin G]]
-[[Category: FEO]]
-[[Category: four-helix bundle]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:52:36 2007''