1n3f: Difference between revisions

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 ==Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence)==
-<StructureSection load='1n3f' size='340' side='right' caption='[[1n3f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1n3f' size='340' side='right'caption='[[1n3f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1n3f]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1n3f]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N3F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1n3e|1n3e]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CR.LSU INTRON OF CHOROPLAST 23S RDNA GENE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3055 CHLRE])</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=1n3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3f OCA], [https://pdbe.org/1n3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n3f RCSB], [https://www.ebi.ac.uk/pdbsum/1n3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3f 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=1n3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3f OCA], [http://pdbe.org/1n3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n3f RCSB], [http://www.ebi.ac.uk/pdbsum/1n3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DNE1_CHLRE DNE1_CHLRE]] Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.
+[https://www.uniprot.org/uniprot/DNE1_CHLRE DNE1_CHLRE] Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.
 == 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/n3/1n3f_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/1n3f_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=1n3f ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Homing endonucleases are highly specific catalysts of DNA strand breaks that induce the transposition of mobile intervening sequences containing the endonuclease open reading frame. These enzymes recognize long DNA targets while tolerating individual sequence polymorphisms within those sites. Sequences of the homing endonucleases themselves diversify to a great extent after founding intron invasion events, generating highly divergent enzymes that recognize similar target sequences. Here, we visualize the mechanism of flexible DNA recognition and the pattern of structural divergence displayed by two homing endonuclease isoschizomers. We determined structures of I-CreI bound to two DNA target sites that differ at eight of 22 base-pairs, and the structure of an isoschizomer, I-MsoI, bound to a nearly identical DNA target site. This study illustrates several principles governing promiscuous base-pair recognition by DNA-binding proteins, and demonstrates that the isoschizomers display strikingly different protein/DNA contacts. The structures allow us to determine the information content at individual positions in the binding site as a function of the distribution of direct and water-mediated contacts to nucleotide bases, and provide an evolutionary snapshot of endonucleases at an early stage of divergence in their target specificity.
-Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI.,Chevalier B, Turmel M, Lemieux C, Monnat RJ Jr, Stoddard BL J Mol Biol. 2003 May 30;329(2):253-69. PMID:12758074<ref>PMID:12758074</ref>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1n3f" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Chlre]]
+[[Category: Chlamydomonas reinhardtii]]
-[[Category: Chevalier, B]]
+[[Category: Large Structures]]
-[[Category: Lemieux, C]]
+[[Category: Chevalier B]]
-[[Category: Monnat, R J]]
+[[Category: Lemieux C]]
-[[Category: Stoddard, B L]]
+[[Category: Monnat RJ]]
-[[Category: Turmel, M]]
+[[Category: Stoddard BL]]
-[[Category: Dna recognition]]
+[[Category: Turmel M]]
-[[Category: Endonuclease]]
-[[Category: Homing]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Laglidadg]]