1gdt: Difference between revisions

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 ==CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA-DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE==
-<StructureSection load='1gdt' size='340' side='right' caption='[[1gdt]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='1gdt' size='340' side='right'caption='[[1gdt]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gdt]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GDT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gdt]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GDT FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TNPR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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]] 3&#8491;</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=1gdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gdt RCSB], [http://www.ebi.ac.uk/pdbsum/1gdt PDBsum]</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=1gdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdt OCA], [https://pdbe.org/1gdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gdt RCSB], [https://www.ebi.ac.uk/pdbsum/1gdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gdt ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TNR1_ECOLI TNR1_ECOLI] This protein catalyzes the site-specific recombination of the transposon and also regulates its frequency of transposition.
 == 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/gd/1gdt_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/1gdt_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=1gdt ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of gamma delta resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 degrees toward the major groove and away from the resolvase catalytic domains at the recombination crossover point. The C-terminal one third of resolvase, which was disordered in the absence of DNA, forms an arm and a 3-helix DNA-binding domain on the opposite side of the DNA from the N-terminal domain. The arms wrap around the minor groove of the central 16 bp, and the DNA-binding domains interact with the major grooves near the outer boundaries of the binding site. The resolvase dimer is asymmetric, particularly in the arm region, implying a conformational adaptability that may be important for resolvase binding to different DNA sites in the synaptosome. It also raises the possibility of a sequential single-strand cleavage mechanism.
-Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.,Yang W, Steitz TA Cell. 1995 Jul 28;82(2):193-207. PMID:7628011<ref>PMID:7628011</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Resolvase|Resolvase]]
+*[[Resolvase 3D structures|Resolvase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Steitz, T A]]
+[[Category: Large Structures]]
-[[Category: Yang, W]]
+[[Category: Steitz TA]]
-[[Category: Dna binding protein-dna complex]]
+[[Category: Yang W]]
-[[Category: Double helix]]
-[[Category: Overhanging base]]
-[[Category: Protein-dna complex]]