3o4p

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<StructureSection load='3o4p' size='340' side='right'caption='[[3o4p]], [[Resolution|resolution]] 0.85&Aring;' scene=''>
<StructureSection load='3o4p' size='340' side='right'caption='[[3o4p]], [[Resolution|resolution]] 0.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3o4p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Common_european_squid Common european squid]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O4P FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3o4p]] 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=3O4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O4P FirstGlance]. <br>
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</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>, <scene name='pdbligand=DXE:1,2-DIMETHOXYETHANE'>DXE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ME2:1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE'>ME2</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.85&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1pjx|1pjx]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DXE:1,2-DIMETHOXYETHANE'>DXE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ME2:1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE'>ME2</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diisopropyl-fluorophosphatase Diisopropyl-fluorophosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.2 3.1.8.2] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o4p OCA], [https://pdbe.org/3o4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o4p RCSB], [https://www.ebi.ac.uk/pdbsum/3o4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o4p ProSAT]</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=3o4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o4p OCA], [https://pdbe.org/3o4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o4p RCSB], [https://www.ebi.ac.uk/pdbsum/3o4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o4p ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BACKGROUND: Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Angstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. RESULTS: A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. CONCLUSIONS: A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism.
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Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase.,Elias M, Liebschner D, Koepke J, Lecomte C, Guillot B, Jelsch C, Chabriere E BMC Res Notes. 2013 Aug 2;6:308. doi: 10.1186/1756-0500-6-308. PMID:23915572<ref>PMID:23915572</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3o4p" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Common european squid]]
 
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[[Category: Diisopropyl-fluorophosphatase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Chabriere, E]]
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[[Category: Loligo vulgaris]]
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[[Category: Elias, M]]
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[[Category: Chabriere E]]
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[[Category: Guillot, B]]
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[[Category: Elias M]]
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[[Category: Jelsch, C]]
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[[Category: Guillot B]]
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[[Category: Koepke, J]]
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[[Category: Jelsch C]]
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[[Category: Lecomte, C]]
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[[Category: Koepke J]]
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[[Category: Liebschner, D]]
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[[Category: Lecomte C]]
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[[Category: Beta-propeller]]
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[[Category: Liebschner D]]
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[[Category: Hydrolase]]
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Current revision

DFPase at 0.85 Angstrom resolution (H atoms included)

PDB ID 3o4p

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