Refinement and structural analysis of barnase at 1.5 angstrom resolution

The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an extr acellular 110-residue enzyme initially solved at 2.0 Angstrom resolution, h as been refined at 1.5 Angstrom using synchrotron radiation and an imaging- plate scanner. Refinement with anisotropic atomic displacement parameters r esulted in increased accuracy of the structure. The final model has a cryst allographic R factor of 11.5% and an R-free of 17.4%. The three independent molecules in the asymmetric unit, referred to as A, B and C, allowed detai led analysis of this final model and meaningful comparison with structures of barnase complexed either with nucleotide inhibitors or with its natural intracellular inhibitor, barstar, The analysis of the overall solvent struc ture revealed a similar number of water molecules associated with each barn ase molecule; among these were 16 equivalent buried solvent molecules, the locations of which are discussed in detail and classified on the basis of t heir structural role. The importance of the water molecules' contribution t o the barnase-barstar interaction is also highlighted. The high accuracy of the present analysis revealed the presence of a Zn2+ ion mediating the con tacts between pairs of symmetry-related A, B or C molecules: such an ion ha d previously only been identified for pairs of C molecules.