July 2017 issue
The crystal structure of the carbapenem-resistance protein CarF has been determined at 1.8 Å resolution. CarF confers partial intrinsic resistance to the naturally occurring antibiotic 1-carbapen-2-em-3-carboxylic acid.
YfeA, a substrate-binding protein that is important for the virulence of Yersinia pestis, has two polyspecific metal-binding sites that may play different roles during infection. A flexible lobe at the carboxy-terminus suggests that structural rearrangement is required for metal transfer to binding partners.
The crystal structure of the cofactor-independent dioxygenase DpgC was refined and the new structure was used to probe the basis for dioxygen binding using site-directed mutagenesis.
Single-wavelength anomalous dispersion (SAD) phasing experiments were successfully carried out at the standard wavelength of 1 Å by using cadmium ions as anomalous scatterers.
Solutions of lysozyme in heavy water with added precipitants were studied by small-angle neutron scattering at lysozyme concentrations of 40, 20 and 10 mg ml−1 and at temperatures of 10, 20 and 30°C. In addition to protein monomers, dimeric and octameric oligomers were also found in solution at the maximal concentration near the optimal crystallization conditions. The volume fraction of octamers decreases on deviation from the optimal temperature and on decreasing the protein concentration. In the absence of the precipitant, only monomers and a minor fraction of dimers are present in solution.
A re-evaluation of m|Fo| − D|Fc| electron-density maps revealed that potential conformational transitions of 27% of DNA phosphates are found in previous crystallographic data. The analysis suggests that some of these unassigned densities correspond to ZI ↔ ZII or A/B → BI transitions.
A seemingly reasonable solution was obtained for the structure of a presumed mutant of an S. typhimurium survival protein (SurE) by molecular replacement using the wild-type SurE structure as the phasing model. Although the crystal was of glycerol dehydrogenase, as subsequently demonstrated using the MarathonMR protocol, the initial structure appeared to be reasonable because of a partial similarity in the arrangement of secondary-structural elements in the two proteins.
Statistical surveys of protein structures reveal that the backbone conformation in terms of (φ, ψ) is the most important factor in τ-angle modulation.