3kgg
From Proteopedia
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| - | {{STRUCTURE_3kgg| PDB=3kgg | SCENE= }} | ||
| - | ===X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): Perdeuteration of proteins for neutron diffraction=== | ||
| - | {{ABSTRACT_PUBMED_20383004}} | ||
| - | == | + | ==X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): Perdeuteration of proteins for neutron diffraction== |
| - | [[http://www.uniprot.org/uniprot/DFPA_LOLVU DFPA_LOLVU | + | <StructureSection load='3kgg' size='340' side='right'caption='[[3kgg]], [[Resolution|resolution]] 2.10Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3kgg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Loligo_vulgaris Loligo vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KGG 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]] 2.1Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kgg OCA], [https://pdbe.org/3kgg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kgg RCSB], [https://www.ebi.ac.uk/pdbsum/3kgg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kgg ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DFPA_LOLVU DFPA_LOLVU] Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).<ref>PMID:15966726</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/kg/3kgg_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=3kgg ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The signal-to-noise ratio is one of the limiting factors in neutron macromolecular crystallography. Protein perdeuteration, which replaces all H atoms with deuterium, is a method of improving the signal-to-noise ratio of neutron crystallography experiments by reducing the incoherent scattering of the hydrogen isotope. Detailed analyses of perdeuterated and hydrogenated structures are necessary in order to evaluate the utility of perdeuterated crystals for neutron diffraction studies. The room-temperature X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase) is reported at 2.1 A resolution. Comparison with an independently refined hydrogenated room-temperature structure of DFPase revealed no major systematic differences, although the crystals of perdeuterated DFPase did not diffract neutrons. The lack of diffraction is examined with respect to data-collection and crystallographic parameters. The diffraction characteristics of successful neutron structure determinations are presented as a guideline for future neutron diffraction studies of macromolecules. X-ray diffraction to beyond 2.0 A resolution appears to be a strong predictor of successful neutron structures. | ||
| - | + | X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.,Blum MM, Tomanicek SJ, John H, Hanson BL, Ruterjans H, Schoenborn BP, Langan P, Chen JC Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Apr 1;66(Pt, 4):379-85. Epub 2010 Mar 26. PMID:20383004<ref>PMID:20383004</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | < | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 3kgg" style="background-color:#fffaf0;"></div> |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Loligo vulgaris]] | [[Category: Loligo vulgaris]] | ||
| - | [[Category: Blum | + | [[Category: Blum M-M]] |
| - | [[Category: Chen | + | [[Category: Chen JC-H]] |
| - | [[Category: Hanson | + | [[Category: Hanson BL]] |
| - | [[Category: John | + | [[Category: John H]] |
| - | [[Category: Langan | + | [[Category: Langan P]] |
| - | [[Category: Schoenborn | + | [[Category: Schoenborn BP]] |
| - | [[Category: Tomanicek | + | [[Category: Tomanicek SJ]] |
| - | [[Category: Terjans | + | [[Category: Terjans HR]] |
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Current revision
X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): Perdeuteration of proteins for neutron diffraction
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Categories: Large Structures | Loligo vulgaris | Blum M-M | Chen JC-H | Hanson BL | John H | Langan P | Schoenborn BP | Tomanicek SJ | Terjans HR
