2id8
From Proteopedia
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| - | [[Image:2id8.gif|left|200px]] | ||
| - | + | ==Crystal structure of Proteinase K== | |
| - | + | <StructureSection load='2id8' size='340' side='right'caption='[[2id8]], [[Resolution|resolution]] 1.27Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | | | + | <table><tr><td colspan='2'>[[2id8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Parengyodontium_album Parengyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ID8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ID8 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]] 1.27Å</td></tr> | |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DB:(S)-(2,3-DIHYDROXYPROPOXY)TRIHYDROXYBORATE'>2DB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=2id8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2id8 OCA], [https://pdbe.org/2id8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2id8 RCSB], [https://www.ebi.ac.uk/pdbsum/2id8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2id8 ProSAT]</span></td></tr> | |
| - | + | </table> | |
| - | + | == Function == | |
| - | + | [https://www.uniprot.org/uniprot/PRTK_PARAQ PRTK_PARAQ] Hydrolyzes keratin at aromatic and hydrophobic residues. | |
| - | + | == 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/id/2id8_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=2id8 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
X-ray single-wavelength anomalous diffraction (SAD) data from a crystal of proteinase K were collected using synchrotron radiation of 0.98 A wavelength at SER-CAT 22-ID beamline, Advanced Photon Source, Argonne National Laboratory. At this wavelength, the expected Bijvoet ratio resulting from the presence of one calcium, one chloride and ten S atoms in the 279-residue protein is extremely small at approximately 0.46%. The direct-methods program SHELXD located 11 anomalous sites using data truncated to 2 A resolution. SHELXE was used to produce an easily interpretable electron-density map. This study shows that an accurate beamline and a good-quality crystal provide the possibility of successfully using a very weak anomalous signal of sulfur measured at a short wavelength for phasing a protein structure, even if a small degree of radiation damage is present. | X-ray single-wavelength anomalous diffraction (SAD) data from a crystal of proteinase K were collected using synchrotron radiation of 0.98 A wavelength at SER-CAT 22-ID beamline, Advanced Photon Source, Argonne National Laboratory. At this wavelength, the expected Bijvoet ratio resulting from the presence of one calcium, one chloride and ten S atoms in the 279-residue protein is extremely small at approximately 0.46%. The direct-methods program SHELXD located 11 anomalous sites using data truncated to 2 A resolution. SHELXE was used to produce an easily interpretable electron-density map. This study shows that an accurate beamline and a good-quality crystal provide the possibility of successfully using a very weak anomalous signal of sulfur measured at a short wavelength for phasing a protein structure, even if a small degree of radiation damage is present. | ||
| - | + | What can be done with a good crystal and an accurate beamline?,Wang J, Dauter M, Dauter Z Acta Crystallogr D Biol Crystallogr. 2006 Dec;62(Pt 12):1475-83. Epub 2006, Nov 23. PMID:17139083<ref>PMID:17139083</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2id8" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Proteinase 3D structures|Proteinase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Parengyodontium album]] | ||
| + | [[Category: Dauter M]] | ||
| + | [[Category: Dauter Z]] | ||
| + | [[Category: Wang J]] | ||
Current revision
Crystal structure of Proteinase K
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