1gef: Difference between revisions

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 ==Crystal structure of the archaeal holliday junction resolvase HJC==
-<StructureSection load='1gef' size='340' side='right' caption='[[1gef]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1gef' size='340' side='right'caption='[[1gef]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gef]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GEF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gef]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GEF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HJC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gef OCA], [http://pdbe.org/1gef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gef RCSB], [http://www.ebi.ac.uk/pdbsum/1gef 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=1gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gef OCA], [https://pdbe.org/1gef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gef RCSB], [https://www.ebi.ac.uk/pdbsum/1gef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gef ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HJC_PYRFU HJC_PYRFU]] A structure-specific endonuclease that resolves Holliday junction (HJ) intermediates during genetic recombination. Cleaves 4-way DNA junctions introducing paired nicks in opposing strands, leaving a 5'-terminal phosphate and a 3'-terminal hydroxyl group that are ligated to produce recombinant products. Cleaves both mobile and immobile junctions. Binds 4-way junction DNA, a synthetic Hj, binding is not competed by dsDNA.[HAMAP-Rule:MF_01490]<ref>PMID:10430863</ref> <ref>PMID:11005813</ref> <ref>PMID:11071944</ref>
+[https://www.uniprot.org/uniprot/HJC_PYRFU HJC_PYRFU] A structure-specific endonuclease that resolves Holliday junction (HJ) intermediates during genetic recombination. Cleaves 4-way DNA junctions introducing paired nicks in opposing strands, leaving a 5'-terminal phosphate and a 3'-terminal hydroxyl group that are ligated to produce recombinant products. Cleaves both mobile and immobile junctions. Binds 4-way junction DNA, a synthetic Hj, binding is not competed by dsDNA.[HAMAP-Rule:MF_01490]<ref>PMID:10430863</ref> <ref>PMID:11005813</ref> <ref>PMID:11071944</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/ge/1gef_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/1gef_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=1gef ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Resolvase|Resolvase]]
+*[[Resolvase 3D structures|Resolvase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43587]]
+[[Category: Large Structures]]
-[[Category: Ishino, Y]]
+[[Category: Pyrococcus furiosus]]
-[[Category: Komori, K]]
+[[Category: Ishino Y]]
-[[Category: Morikawa, K]]
+[[Category: Komori K]]
-[[Category: Nishino, T]]
+[[Category: Morikawa K]]
-[[Category: Tsuchiya, D]]
+[[Category: Nishino T]]
-[[Category: Hjc]]
+[[Category: Tsuchiya D]]
-[[Category: Holliday junction resolvase]]
-[[Category: Hydrolase]]