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 Powers; Theresa 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

doi:10.1002/pro.2774

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 journal › Review article › peer-review

22 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 language	English (US)
Pages (from-to)	30-45
Number of pages	16
Journal	Protein Science
Volume	25
Issue number	1
DOIs	https://doi.org/10.1002/pro.2774
State	Published - 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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10.1002/pro.2774

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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

Everett, JK, Tejero, R, Murthy, SBK, Acton, TB, Aramini, JM, Baran, MC, Benach, J, Cort, JR, Eletsky, A, Forouhar, F, Guan, R, Kuzin, AP, Lee, HW, Liu, G, Mani, R, Mao, B, Mills, JL, Montelione, AF, Pederson, K, Powers, R, Ramelot, T, Rossi, P, Seetharaman, J, Snyder, D, Swapna, GVT, Vorobiev, SM, Wu, Y, Xiao, R, Yang, Y, Arrowsmith, CH, Hunt, JF, Kennedy, MA, Prestegard, JH, Szyperski, T, Tong, L & Montelione, GT 2016, 'A community resource of experimental data for NMR / X-ray crystal structure pairs', Protein Science, vol. 25, no. 1, pp. 30-45. https://doi.org/10.1002/pro.2774

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title = "A community resource of experimental data for NMR / X-ray crystal structure pairs",

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.",

keywords = "X-ray crystallography, accuracy and precision of NMR structures, protein NMR spectroscopy, structural bioinformatics",

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

note = "Publisher Copyright: {\textcopyright} 2015 The Protein Society.",

year = "2016",

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doi = "10.1002/pro.2774",

language = "English (US)",

volume = "25",

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AU - Everett, John K.

AU - Tejero, Roberto

AU - Murthy, Sarath B.K.

AU - Acton, Thomas B.

AU - Aramini, James M.

AU - Baran, Michael C.

AU - Benach, Jordi

AU - Cort, John R.

AU - Eletsky, Alexander

AU - Forouhar, Farhad

AU - Guan, Rongjin

AU - Kuzin, Alexandre P.

AU - Lee, Hsiau Wei

AU - Liu, Gaohua

AU - Mani, Rajeswari

AU - Mao, Binchen

AU - Mills, Jeffrey L.

AU - Montelione, Alexander F.

AU - Pederson, Kari

AU - Powers, Robert

AU - Ramelot, Theresa

AU - Rossi, Paolo

AU - Seetharaman, Jayaraman

AU - Snyder, David

AU - Swapna, G. V.T.

AU - Vorobiev, Sergey M.

AU - Wu, Yibing

AU - Xiao, Rong

AU - Yang, Yunhuang

AU - Arrowsmith, Cheryl H.

AU - Hunt, John F.

AU - Kennedy, Michael A.

AU - Prestegard, James H.

AU - Szyperski, Thomas

AU - Tong, Liang

AU - Montelione, Gaetano T.

PY - 2016/1/1

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N2 - 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.

AB - 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.

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KW - accuracy and precision of NMR structures

KW - protein NMR spectroscopy

KW - structural bioinformatics

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JO - Protein Science

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ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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