4yta
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<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> | <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" 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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2Å</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='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'>[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> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN] | [https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | 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. | ||
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| - | 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> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4yta" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Trypsin 3D structures|Trypsin 3D structures]] | *[[Trypsin 3D structures|Trypsin 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
BOND LENGTH ANALYSIS OF ASP, GLU AND HIS RESIDUES IN TRYPSIN AT 1.2A RESOLUTION
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