1vkq

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(New page: 200px<br /><applet load="1vkq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vkq, resolution 1.60&Aring;" /> '''A re-determination o...)
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[[Image:1vkq.jpg|left|200px]]<br /><applet load="1vkq" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1vkq, resolution 1.60&Aring;" />
 
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'''A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength'''<br />
 
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==Overview==
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==A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength==
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The crystal structure of the triple mutant K53,56,120M of bovine, pancreatic phospholipase A(2) has been redetermined using sulfur, single-wavelength anomalous scattering. The synchrotron data were, collected at lambda = 1.54 A and the crystal diffracted to 1.6 A, resolution. The program SOLVE was used to locate the heavy atoms and to, estimate the initial phases and the resulting map was then subjected to, RESOLVE. The output of 455 non-H atoms, including 12 S atoms, one calcium, ion and one chloride ion, were then subjected to ARP/wARP followed by, REFMAC. With the improved phases, the automatic model building, successfully built more than 85% of the 123 residues, excluding the N- and, C-terminal residues. The final crystallographic R factor is 17.7% (R(free), = 21.7%). The refined model consists of 954 non-H protein atoms, 165 water, O atoms, three 2-methyl-2,4-pentanediol (MPD) molecules, one calcium ion, and one chloride ion. The present work is yet another example that shows, the utility of single-wavelength anomalous scattering data for solving a, protein structure.
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<StructureSection load='1vkq' size='340' side='right'caption='[[1vkq]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1vkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VKQ FirstGlance]. <br>
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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]] 1.6&#8491;</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vkq OCA], [https://pdbe.org/1vkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vkq RCSB], [https://www.ebi.ac.uk/pdbsum/1vkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vkq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PA21B_BOVIN PA21B_BOVIN] PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/1vkq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1vkq ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of the triple mutant K53,56,120M of bovine pancreatic phospholipase A(2) has been redetermined using sulfur single-wavelength anomalous scattering. The synchrotron data were collected at lambda = 1.54 A and the crystal diffracted to 1.6 A resolution. The program SOLVE was used to locate the heavy atoms and to estimate the initial phases and the resulting map was then subjected to RESOLVE. The output of 455 non-H atoms, including 12 S atoms, one calcium ion and one chloride ion, were then subjected to ARP/wARP followed by REFMAC. With the improved phases, the automatic model building successfully built more than 85% of the 123 residues, excluding the N- and C-terminal residues. The final crystallographic R factor is 17.7% (R(free) = 21.7%). The refined model consists of 954 non-H protein atoms, 165 water O atoms, three 2-methyl-2,4-pentanediol (MPD) molecules, one calcium ion and one chloride ion. The present work is yet another example that shows the utility of single-wavelength anomalous scattering data for solving a protein structure.
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==About this Structure==
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A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength.,Sekar K, Rajakannan V, Velmurugan D, Yamane T, Thirumurugan R, Dauter M, Dauter Z Acta Crystallogr D Biol Crystallogr. 2004 Sep;60(Pt 9):1586-90. Epub 2004, Aug 26. PMID:15333929<ref>PMID:15333929</ref>
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1VKQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with CA, CL and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VKQ OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength., Sekar K, Rajakannan V, Velmurugan D, Yamane T, Thirumurugan R, Dauter M, Dauter Z, Acta Crystallogr D Biol Crystallogr. 2004 Sep;60(Pt 9):1586-90. Epub 2004, Aug 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15333929 15333929]
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</div>
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[[Category: Bos taurus]]
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<div class="pdbe-citations 1vkq" style="background-color:#fffaf0;"></div>
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[[Category: Phospholipase A(2)]]
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[[Category: Single protein]]
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[[Category: Dauter, M.]]
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[[Category: Dauter, Z.]]
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[[Category: Rajakannan, V.]]
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[[Category: Sekar, K.]]
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[[Category: Velmurugan, D.]]
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[[Category: Yamane, T.]]
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[[Category: CA]]
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[[Category: CL]]
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[[Category: MPD]]
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[[Category: alpha helix]]
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[[Category: beta sheet]]
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[[Category: calcium ion]]
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[[Category: triple mutant]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:55:24 2007''
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==See Also==
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*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bos taurus]]
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[[Category: Large Structures]]
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[[Category: Dauter M]]
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[[Category: Dauter Z]]
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[[Category: Rajakannan V]]
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[[Category: Sekar K]]
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[[Category: Velmurugan D]]
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[[Category: Yamane T]]

Current revision

A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength

PDB ID 1vkq

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