Protein structure refinement: Streptomyces griseus serine protease A at 1.8 Å resolution

Abstract

The crystal structure of the bacterial serine protease from Streptomyces griseus (SGPA) has been refined at 1.8 Å resolution by a restrained parameter least-squares procedure ( Konnert, 1976) to a conventional R factor of 0.139 for 12662 statistically significant reflections [ I > 3 σ( I)]. The number of variable parameters in the final model was 5912 which included positional and individual thermal parameters of the enzyme, and positions, B factors and occupancies of 175 solvent molecules. The algorithm used for this refinement allows for the simultaneous restraint on bond distances and distances related to interbond angles, the coplanarity of atoms in planar groups, the conservation of chirality of asymmetric centres, non-bonded contact distances, conformational torsional angles and individual isotropic temperature factors. The refined structure of SGPA differs from ideal bond lengths by an overall root-mean-square deviation of 0.02 Å; the corresponding value for angle distances is 0.038 Å. Comparison of the phase angles for the shell of data, 8.0 to 2.8 Å, between the multiple isomorphous replacement phases (Brayer et al., 1978 a) and the refined phases, indicates an overall difference (r.m.s.) of 56.6 °. The average conformational angle of the peptide bond (ω) is 179.7 ° (root-mean-square deviation ± 2.5 °) for the 180 peptide bonds of SGPA. Of the 175 solvent molecules included during the course of the refinement, 22 with occupancies ranging from 1.00 to 0.38 are located in the active site and the substrate binding region. It was not until these water molecules were included in the refinement process that the active Ser195 adopted its final conformation ( χ 1 = −77 °). The resulting distance from O γ of Ser195 to N ε 2 of His57 is 3.1 Å, which, when taken with the observed distortion from linearity (50 °), indicates a rather weak interaction.