1dy5
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(New page: 200px<br /><applet load="1dy5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dy5, resolution 0.87Å" /> '''DEAMIDATED DERIVATIV...)
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Revision as of 11:33, 20 November 2007
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DEAMIDATED DERIVATIVE OF BOVINE PANCREATIC RIBONUCLEASE
Overview
Crystals of the deamidated form of bovine pancreatic ribonuclease which, contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100, K. We have refined the crystallographic model using anisotropic, displacement parameters for all atoms to a conventional crystallographic, residual R=0.101 for all observed reflections in the resolution range, 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model., This structure represents one of the highest resolution protein structures, to date and interestingly, it is the only example containing more than one, molecule in the asymmetric unit with a resolution better than 1.0 A. The, non-crystallographic symmetry has been used as a validation check of the, geometrical parameters and it has allowed an estimate for an upper limit, of errors associated with this high resolution model. In the present, structure it was possible to obtain a more accurate picture of the active, site whose electron density was not clearly interpretable in the previous, 1.9 A resolution structure. In particular, the P1 site is alternatively, occupied either by a sulphate anion or by a water molecule network. Most, of hydrogen atoms were visible in the electron density maps, including, those involved in C(alpha)-H(alpha).O interactions. Analysis of, protein-solvent interactions has revealed the occurrence of an extensive, cluster of water molecules, predominantly arranged in pentagonal fused, rings and surrounding hydrophobic moiety of side-chains. Finally, in spite, of the limited sample of residues, we have detected a clear dependence of, backbone N-C(alpha)-C angle on residue conformation. This correlation can, be fruitfully used as a valuable tool in protein structure validation.
About this Structure
1DY5 is a Single protein structure of sequence from Bos taurus with SO4, ACT and IPA as ligands. Active as Pancreatic ribonuclease, with EC number 3.1.27.5 Full crystallographic information is available from OCA.
Reference
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis., Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L, J Mol Biol. 2000 Mar 31;297(3):713-32. PMID:10731423
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