Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 A resolution

Abstract

Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 A resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic least-squares refinement with SHELXL gave a final conventional R factor of 10.51% for all reflections in the 15-1.15 A resolution range. The estimated r.m.s. errors of the model are 0.026 and 0.038 A for protein atoms and all atoms, respectively. The structure comprises all 310 amino acids, with 28 side chains and two peptide bonds in multiple conformations, two covalently linked Pb atoms, 601 water molecules, seven glycerol molecules, one sulfate ion and two chloride ions. Water molecules accounting for alternative solvent structure are modelled with a fixed occupancy of 0.5. The structure is described in detail and compared with previously reported dehalogenase structures refined at 1.9-2.3 A resolution. An analysis of the protein's geometry and stereochemistry reveals eight mean values of bond lengths and angles which deviate significantly from the Engh & Huber parameters, a wide spread in the main-chain omega torsion angle around its ideal value of 180 (6) degrees and a role for C-HcO interactions in satisfying the hydrogen-bond acceptor capacity of main-chain carbonyl O atoms in the central beta-sheet.