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Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W. A public database of macromolecular diffraction experiments. Acta Crystallogr D Struct Biol 2016; 72:1181-1193. [PMID: 27841751 PMCID: PMC5108346 DOI: 10.1107/s2059798316014716] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/17/2016] [Indexed: 12/28/2022] Open
Abstract
The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Karol M. Langner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Piotr Sroka
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 90237, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank; Center for Integrative Proteomics Research; Institute for Quantitative Biomedicine; Rutgers Cancer Institute of New Jersey; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- San Diego Supercomputer Center and Skaggs School of Pharmacological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
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Abstract
Metal ions play a key role in nucleic acid structure and activity. Elucidation of the rules that govern the binding of metal ions is therefore an essential step for better understanding of the nucleic acid functions. This review is as an update to a preceding one (Metal Ions Biol. Syst., 1996, 32, 91-134), in which we offered a general view of metal ion interactions with mono-, di-, tri-, and oligonucleotides in the solid state, based on their crystal structures reported before 1994. In this chapter, we survey all the crystal structures of metal ion complexes with nucleotides involving oligonucleotides reported after 1994 and we have tried to uncover new characteristic metal bonding patterns for mononucleotides and oligonucleotides with A-RNA and A/B/Z-DNA fragments that form duplexes. We do not cover quadruplexes, duplexes with metal-mediated base-pairs, tRNAs, rRNAs in ribosome, ribozymes, and nucleic acid-drug and -protein complexes. Factors that affect metal binding to mononucleotides and oligonucleotide duplexes are also dealt with.
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