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Exploiting tertiary structure through local folds for crystallographic phasing

Nature Methods volume 10, pages 1099–1101 (2013)Cite this article

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A Corrigendum to this article was published on 27 June 2014

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Abstract

We describe an algorithm for phasing protein crystal X-ray diffraction data that identifies, retrieves, refines and exploits general tertiary structural information from small fragments available in the Protein Data Bank. The algorithm successfully phased, through unspecific molecular replacement combined with density modification, all-helical, mixed alpha-beta, and all-beta protein structures. The method is available as a software implementation: Borges.

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Figure 1: Characteristic Cα-O vectors (CVs) used in Borges to handle secondary structure and local fold geometry.
Figure 2: Overall occurrence of model fragments and their role in phasing an all-beta and a previously unknown structure.

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Protein Data Bank

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Protein Data Bank

Swiss-Prot

Change history

  • 05 May 2014

    In the version of this article initially published, the authors did not acknowledge all of the people involved in the generation of the crystallographic data set of AF1503 from A. fulgidus. These diffraction data were originated by M. Hulko, A. Ursinus, K. Bär, J. Martin, K.Z. and A.N. Lupas at the Max Planck Institute for Developmental Biology, Tübingen. M. Hulko, A. Ursinus, K. Bär, J. Martin and A.N. Lupas have kindly given their retroactive permission to use the data. Their report on the AF1503 structure was published in the Journal of Structural Biology (doi:10.1016/j.jsb.2014.02.008) and PDB 4CQ4. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

This work was supported by the Spanish Ministerio de Ciencia e Innovación-Ministerio de Economia y Competitividad, Centro de Desarrollo Tecnológico Industrial and Consejo Superior de Investigaciones Científicas (grants BIO2009-10576; IDC-2010-1173; BFU2012-35367; BFU2012-32847; predoctoral grants to D.D.R., I.D.M. and I.M.d.I.; JdC to K.M.; RyC to R.M.B.); Generalitat de Catalunya (2009SGR-1036); VW-Stiftung Niedersachsenprofessur to G.M.S. We also acknowledge beam time on the Swiss Light Source beamline X10SA and computing time at the FCSCL. We thank M. Hulko, A. Ursinus, K. Bär, J. Martin and A.N. Lupas at the Max Planck Institute for Developmental Biology, Tübingen, for permission to use the diffraction data of AF1503 from A. fulgidus.

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Authors and Affiliations

  1. Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain

    Massimo Sammito, Claudia Millán, Dayté D Rodríguez, Iñaki M de Ilarduya, Kathrin Meindl, Ivan De Marino, Giovanna Petrillo & Isabel Usón

  2. Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas–Universidad de Salamanca, Salamanca, Spain

    Rubén M Buey & José M de Pereda

  3. Ikerbasque Basque Foundation for Science at Unidad de Biofísica, Consejo Superior de Investigaciones Científicas–Universidad del País Vasco, Leioa, Spain

    Kornelius Zeth

  4. Lehrstuhl für Strukturchemie, Universität Göttingen, Göttingen, Germany

    George M Sheldrick

  5. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain

    Isabel Usón

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  1. Massimo Sammito
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All authors contributed extensively to the work presented in this paper.

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Correspondence to Isabel Usón.

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Supplementary Figures 1 and 2, Supplementary Tables 1 and 2, Supplementary Results and Supplementary Notes 1 and 2 (PDF 6443 kb)

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Sammito, M., Millán, C., Rodríguez, D. et al. Exploiting tertiary structure through local folds for crystallographic phasing. Nat Methods 10, 1099–1101 (2013). https://doi.org/10.1038/nmeth.2644

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