The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.

Central European Institute of Technology CEITEC Masaryk University Kamenice 5 A4 62500 Brno Czech Republic

Department of Biochemistry Faculty of Science Masaryk University Kamenice 5 A5 62500 Brno Czech Republic

Laboratory of Molecular Genetics of Bacteria Institute of Microbiology Academy of Sciences of the Czech Republic Vídeňská 1083 142 20 Prague Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 A4 62500 Brno Czech Republic

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