4yta: Difference between revisions

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 ==BOND LENGTH ANALYSIS OF ASP, GLU AND HIS RESIDUES IN TRYPSIN AT 1.2A RESOLUTION==
-<StructureSection load='4yta' size='340' side='right' caption='[[4yta]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+<StructureSection load='4yta' size='340' side='right'caption='[[4yta]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4yta]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YTA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4yta]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3unr 3unr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YTA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3unr|3unr]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></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=4yta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yta OCA], [https://pdbe.org/4yta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yta RCSB], [https://www.ebi.ac.uk/pdbsum/4yta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yta ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yta OCA], [http://pdbe.org/4yta PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yta RCSB], [http://www.ebi.ac.uk/pdbsum/4yta PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yta ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
-A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 A for trypsin (97% complete, 12% H-atom visibility at 2.5sigma), 1.26 A for subtilisin (100% complete, 11% H-atom visibility at 2.5sigma) and 0.65 A for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3sigma). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 A and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 A resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 A resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.
-Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.,Fisher SJ, Blakeley MP, Cianci M, McSweeney S, Helliwell JR Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):800-9. doi:, 10.1107/S0907444912012589. Epub 2012 Jun 15. PMID:22751665<ref>PMID:22751665</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4yta" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Trypsin|Trypsin]]
+*[[Trypsin 3D structures|Trypsin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Bos taurus]]
-[[Category: Trypsin]]
+[[Category: Large Structures]]
-[[Category: Blakeley, M P]]
+[[Category: Blakeley MP]]
-[[Category: Cianci, M]]
+[[Category: Cianci M]]
-[[Category: Fisher, S J]]
+[[Category: Fisher SJ]]
-[[Category: Helliwell, J R]]
+[[Category: Helliwell JR]]
-[[Category: McSweeny, S]]
+[[Category: McSweeny S]]
-[[Category: Hydrolase]]
-[[Category: Serine protease]]