PNNL

Abstract

The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. While a primary goal, for the sake of efficiency, was to provide at least one structure from each of the targeted domain families, in some cases structures were determined by both NMR and X-ray crystallography for the identical (or nearly identical) protein construct. NMR spectroscopy and X-ray diffraction data for these 43 “NMR / X-ray” structure pairs have been organized on an NMR / X-ray Structure Pair Data Base. As an example of the utility of this data base, these data were also used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and co-workers several years ago (M. Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy, R. (2007) PROTEINS 69: 449 – 465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. However structural differences are observed between some of these NMR structures and the corresponding X-ray crystal structures. It is anticipated that the NMR / X-ray Structure Pair Data Data Base will provide a valuable resource for new methods development.