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Insights from soft X-rays: the chlorine and sulfur sub-structures of a CK2α/DRB complex

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Abstract

The diffraction pattern of a protein crystal is normally a product of the interference of electromagnetic waves scattered by electrons of the crystalline sample. The diffraction pattern undergoes systematic changes in case additionally X-ray absorption occurs, meaning if the wavelength of the primary X-ray beam is relatively close to the absorption edge of selected elements of the sample. The resulting effects are summarized as “anomalous dispersion” and can be always observed with “soft” X-rays (wavelength around 2 Å) since they match the absorption edges of sulfur and chlorine. A particularly useful application of this phenomenon is the experimental detection of the sub-structures of the anomalous scatterers in protein crystals. We demonstrate this here with a crystal of a C-terminally truncated variant of human CK2α to which two molecules of the inhibitor 5,6-dichloro-1-β-d-ribo-furanosyl-benzimidazole (DRB) are bound. The structure of this co-crystal has been solved recently. For this study we measured an additional diffraction data set at a wavelength of 2 Å which showed strong anomalous dispersion effects. On the basis of these effects we detected all sulfur atoms of the protein, the two liganded DRB molecules and a total of 16 additional chloride ions some of them emerging at positions filled with water molecules in previous structure determinations. A number of chloride ions are bound to structural and functional important locations fitting to the constitutive activity and the acidophilic substrate specificity of the enzyme.

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Acknowledgments

We are grateful to Dr. Manfred Weiss and Dr. Annette Faust for assistance at beamline X12 of the EMBL outstation in Hamburg, Germany. This work was funded by the Deutsche Forschungsgemeinschaft (grant NI 643/1-3) and by the Forskningsråd for Natur og Univers (grant 272-07-0257).

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Authors and Affiliations

  1. Universität zu Köln, Institut für Biochemie, Zülpicher Straße 47, 50674, Köln, Germany

    Jennifer Raaf & Karsten Niefind

  2. Syddansk Universitet, Institut for Biokemi og Molekylær Biologi, Campusvej 55, 5230, Odense, Denmark

    Olaf-Georg Issinger

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  1. Jennifer Raaf
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  2. Olaf-Georg Issinger
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Correspondence to Karsten Niefind.

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Raaf, J., Issinger, OG. & Niefind, K. Insights from soft X-rays: the chlorine and sulfur sub-structures of a CK2α/DRB complex. Mol Cell Biochem 316, 15–23 (2008). https://doi.org/10.1007/s11010-008-9826-1

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  • DOI: https://doi.org/10.1007/s11010-008-9826-1

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