Structures of Four Crystal Forms of Decaplanin

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Abstract

The glycopeptide antibiotic decaplanin (1; formerly known as MM 47761 and M86-1410) crystallizes in two P21 and two P6122 crystal forms, each with four monomers in the asymmetric unit, with solvent contents varying from 48 to 69%. Although with ca. 600 unique atoms, the structures are larger than typical small molecules, one was solved by direct methods. The other three were solved by typical macromolecular methods: single-wavelength anomalous diffraction (SAD) of the Cl-atoms present naturally in the structure, multiple-wavelength anomalous diffraction (MAD) at the Br absorption edge for a crystal soaked in NaBr solution, and molecular replacement. There is evidence of appreciable radiation damage with loss of 20–30% of the covalent and ionic halogens affecting the synchrotron datasets that may even have unintentionally facilitated the MAD structure solution. The structures contain the dimer units typical of antibiotics related to vancomycin, but, in addition, there are a variety of further intermolecular interactions responsible for the polymorphy leading to intertwined 61-helices in two of the crystal forms. Except for the sugars and some sidechains, the conformations of the 16 independent monomers are very similar.

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