2prk: Difference between revisions

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OCA

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-[[Image:2prk.jpg|left|200px]]<br /><applet load="2prk" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2prk, resolution 1.5&Aring;" />
-'''SYNCHROTRON X-RAY DATA COLLECTION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF PROTEINASE K AT 1.5 ANGSTROMS RESOLUTION'''<br />
-==Overview==
+==SYNCHROTRON X-RAY DATA COLLECTION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF PROTEINASE K AT 1.5 ANGSTROMS RESOLUTION==
-The structure of the serine endopeptidase proteinase K (279 amino acid, residues; 28,790 daltons) has been refined by restrained least-squares, methods to a conventional R value of 16.7% employing synchrotron film data, of 30,812 reflections greater than 3 sigma in the 5.0 to 1.5 A resolution, range. During refinement, the molecular structure was restrained to known, stereochemistry, with root-mean-square (r.m.s.) deviation of 0.015 A from, ideal bond lengths. The average atomic temperature factor, B, is 11.1 A2, for all atoms. The final model comprises 2020 protein atoms and 174, solvent molecules (which were given unit occupancies). Four corrections to, the amino acid sequence were made, which were confirmed later by sequence, analysis of the proteinase K gene: a deletion of one glycine in position, 80; a change of sequence in position 207-208 and insertions of the, dipeptide 210-211 and of residue 270. The r.m.s. deviation in the alpha-C, atomic positions between the final refined model and the initial model, built on the basis of a 3.3 A mini-map is 1.72 A for 227 out of 266, residues, which were originally traced in the mini-map without sequence, information. The positions of the remaining 39 residues deviate by more, than 8 A from the original ones and are located in regions where extensive, revision of the structural model was necessary.
+<StructureSection load='2prk' size='340' side='right'caption='[[2prk]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2prk]] 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=2PRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PRK 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]] 1.5&#8491;</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></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=2prk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2prk OCA], [https://pdbe.org/2prk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2prk RCSB], [https://www.ebi.ac.uk/pdbsum/2prk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2prk 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/pr/2prk_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=2prk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the serine endopeptidase proteinase K (279 amino acid residues; 28,790 daltons) has been refined by restrained least-squares methods to a conventional R value of 16.7% employing synchrotron film data of 30,812 reflections greater than 3 sigma in the 5.0 to 1.5 A resolution range. During refinement, the molecular structure was restrained to known stereochemistry, with root-mean-square (r.m.s.) deviation of 0.015 A from ideal bond lengths. The average atomic temperature factor, B, is 11.1 A2 for all atoms. The final model comprises 2020 protein atoms and 174 solvent molecules (which were given unit occupancies). Four corrections to the amino acid sequence were made, which were confirmed later by sequence analysis of the proteinase K gene: a deletion of one glycine in position 80; a change of sequence in position 207-208 and insertions of the dipeptide 210-211 and of residue 270. The r.m.s. deviation in the alpha-C atomic positions between the final refined model and the initial model built on the basis of a 3.3 A mini-map is 1.72 A for 227 out of 266 residues, which were originally traced in the mini-map without sequence information. The positions of the remaining 39 residues deviate by more than 8 A from the original ones and are located in regions where extensive revision of the structural model was necessary.
-==About this Structure==
+Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution.,Betzel C, Pal GP, Saenger W Acta Crystallogr B. 1988 Apr 1;44 ( Pt 2):163-72. PMID:3271105<ref>PMID:3271105</ref>
-PRK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PRK OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution., Betzel C, Pal GP, Saenger W, Acta Crystallogr B. 1988 Apr 1;44 ( Pt 2):163-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3271105 3271105]
+</div>
-[[Category: Engyodontium album]]
+<div class="pdbe-citations 2prk" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Subtilisin]]
-[[Category: Betzel, C.]]
-[[Category: Pal, G.P.]]
-[[Category: Saenger, W.]]
-[[Category: CA]]
-[[Category: serine proteinase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:38:10 2007''
+==See Also==
+*[[Proteinase 3D structures|Proteinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Parengyodontium album]]
+[[Category: Betzel C]]
+[[Category: Pal GP]]
+[[Category: Saenger W]]