The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis.
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.
Esposito
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Centro di Studio di Biocristallografia, CNR and Dipartimento di Chimica Università di Napoli "Federico II", Via Mezzocannone 4 I-80134, Napoli, Italy.
Vitagliano
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Sica
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Sorrentino
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Zagari
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Mazzarella
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D000577:Amides / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D016880:Anisotropy; D001224:Aspartic Acid / Q000378:metabolism*; D001665:Binding Sites; D002417:Cattle; D003460:Crystallization; D018360:Crystallography, X-Ray; D005973:Glutamine / Q000378:metabolism; D006639:Histidine / Q000378:metabolism; D006859:Hydrogen / Q000378:metabolism; D006860:Hydrogen Bonding; D008239:Lysine / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012259:Ribonuclease, Pancreatic / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents; D013431:Sulfates / Q000378:metabolism; D014867:Water / Q000378:metabolism*
D000577:Amides; D012997:Solvents; D013431:Sulfates; D014867:Water; D005973:Glutamine; D001224:Aspartic Acid; D006639:Histidine; D006859:Hydrogen; D012259:Ribonuclease, Pancreatic; D008239:Lysine