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==A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT== | |||
<StructureSection load='1ayp' size='340' side='right'caption='[[1ayp]], [[Resolution|resolution]] 2.57Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ayp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AYP 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]] 2.57Å</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=INB:1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL+SULFIDE'>INB</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=1ayp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayp OCA], [https://pdbe.org/1ayp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ayp RCSB], [https://www.ebi.ac.uk/pdbsum/1ayp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayp ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PA2GA_HUMAN PA2GA_HUMAN] Thought to participate in the regulation of the phospholipid metabolism in biomembranes including eicosanoid biosynthesis. Catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. | |||
== 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/ay/1ayp_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ayp ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
It is often found in the crystallization of enzyme-inhibitor complexes that an inhibitor causes crystal packing which is different to that of native protein. This is the case for crystals of human non-pancreatic secreted phospholipase A(2) (124 residues) containing six molecules in the asymmetric unit when the protein is complexed with a potential acylamino analogue of a phospholid. The hexameric structure was determined by molecular replacement using the structure of monomeric native protein as a probe. As an extension to the experiment, it was tested whether a backbone polypeptide composed of 17% of a known monomeric structure could find its correct position on a target molecule in molecular replacement. A probe model composed of the backbone atoms of the N-terminal 77 residues of lysine-, arginine-, ornithine-binding protein (LAO, a total of 238 residues) liganded with lysine correctly finds its position on LAO liganded with histidine which crystallizes as a monomer in the asymmetric unit. The results indicate that as little as 17% of total diffracting matter can be used in molecular replacement to solve crystal structures or to obtain phase information which can be combined with phases obtained by the isomorphous-replacement method. | |||
A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement.,Oh BH Acta Crystallogr D Biol Crystallogr. 1995 Mar 1;51(Pt 2):140-4. PMID:15299314<ref>PMID:15299314</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1ayp" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Oh | [[Category: Oh B-H]] | ||
Latest revision as of 07:23, 17 October 2024
A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENTA PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT
Structural highlights
FunctionPA2GA_HUMAN Thought to participate in the regulation of the phospholipid metabolism in biomembranes including eicosanoid biosynthesis. Catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIt is often found in the crystallization of enzyme-inhibitor complexes that an inhibitor causes crystal packing which is different to that of native protein. This is the case for crystals of human non-pancreatic secreted phospholipase A(2) (124 residues) containing six molecules in the asymmetric unit when the protein is complexed with a potential acylamino analogue of a phospholid. The hexameric structure was determined by molecular replacement using the structure of monomeric native protein as a probe. As an extension to the experiment, it was tested whether a backbone polypeptide composed of 17% of a known monomeric structure could find its correct position on a target molecule in molecular replacement. A probe model composed of the backbone atoms of the N-terminal 77 residues of lysine-, arginine-, ornithine-binding protein (LAO, a total of 238 residues) liganded with lysine correctly finds its position on LAO liganded with histidine which crystallizes as a monomer in the asymmetric unit. The results indicate that as little as 17% of total diffracting matter can be used in molecular replacement to solve crystal structures or to obtain phase information which can be combined with phases obtained by the isomorphous-replacement method. A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement.,Oh BH Acta Crystallogr D Biol Crystallogr. 1995 Mar 1;51(Pt 2):140-4. PMID:15299314[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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