A community resource of experimental data for NMR / X-ray crystal structure pairs

John K. Everett, Roberto Tejero, Sarath B.K. Murthy, Thomas B. Acton, James M. Aramini, Michael C. Baran, Jordi Benach, John R. Cort, Alexander Eletsky, Farhad Forouhar, Rongjin Guan, Alexandre P. Kuzin, Hsiau Wei Lee, Gaohua Liu, Rajeswari Mani, Binchen Mao, Jeffrey L. Mills, Alexander F. Montelione, Kari Pederson, Robert PowersTheresa Ramelot, Paolo Rossi, Jayaraman Seetharaman, David Snyder, G. V.T. Swapna, Sergey M. Vorobiev, Yibing Wu, Rong Xiao, Yunhuang Yang, Cheryl H. Arrowsmith, John F. Hunt, Michael A. Kennedy, James H. Prestegard, Thomas Szyperski, Liang Tong, Gaetano T. Montelione

Research output: Contribution to journalReview article

6 Scopus citations

Abstract

We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. 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. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;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. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.

Original languageEnglish (US)
Pages (from-to)30-45
Number of pages16
JournalProtein Science
Volume25
Issue number1
DOIs
StatePublished - Jan 1 2016

Keywords

  • X-ray crystallography
  • accuracy and precision of NMR structures
  • protein NMR spectroscopy
  • structural bioinformatics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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    Everett, J. K., Tejero, R., Murthy, S. B. K., Acton, T. B., Aramini, J. M., Baran, M. C., Benach, J., Cort, J. R., Eletsky, A., Forouhar, F., Guan, R., Kuzin, A. P., Lee, H. W., Liu, G., Mani, R., Mao, B., Mills, J. L., Montelione, A. F., Pederson, K., ... Montelione, G. T. (2016). A community resource of experimental data for NMR / X-ray crystal structure pairs. Protein Science, 25(1), 30-45. https://doi.org/10.1002/pro.2774