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2id8

From Proteopedia

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[[Image:2id8.gif|left|200px]]
 
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{{Structure
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==Crystal structure of Proteinase K==
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|PDB= 2id8 |SIZE=350|CAPTION= <scene name='initialview01'>2id8</scene>, resolution 1.27&Aring;
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<StructureSection load='2id8' size='340' side='right'caption='[[2id8]], [[Resolution|resolution]] 1.27&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <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>
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<table><tr><td colspan='2'>[[2id8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Engyodontium_album Engyodontium 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>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </span>
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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=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>
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|GENE=
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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/Peptidase_K Peptidase K], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </span></td></tr>
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|DOMAIN=
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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=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>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2id8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2id8 OCA], [http://www.ebi.ac.uk/pdbsum/2id8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2id8 RCSB]</span>
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== Function ==
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}}
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[[https://www.uniprot.org/uniprot/PRTK_TRIAL PRTK_TRIAL]] Hydrolyzes keratin at aromatic and hydrophobic residues.
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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/id/2id8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2id8 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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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.
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'''Crystal structure of Proteinase K'''
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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&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 2id8" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Proteinase|Proteinase]]
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*[[Proteinase 3D structures|Proteinase 3D structures]]
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==About this Structure==
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== References ==
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2ID8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ID8 OCA].
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<references/>
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17139083 17139083]
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[[Category: Engyodontium album]]
[[Category: Engyodontium album]]
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[[Category: Large Structures]]
[[Category: Peptidase K]]
[[Category: Peptidase K]]
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[[Category: Single protein]]
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[[Category: Dauter, M]]
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[[Category: Dauter, M.]]
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[[Category: Dauter, Z]]
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[[Category: Dauter, Z.]]
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[[Category: Wang, J]]
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[[Category: Wang, J.]]
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[[Category: Hydrolase]]
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[[Category: proteinase]]
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[[Category: Proteinase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:42:43 2008''
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Current revision

Crystal structure of Proteinase K

PDB ID 2id8

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