Abstract
Partial symmetry, i.e., the presence of more than one molecule in the asymmetric unit of a crystal, is a relatively rare phenomenon in small-molecule crystallography, but is quite common in protein crystallography, where it is typically known as non-crystallographic symmetry (NCS). Several papers in literature propose molecular determinants such as crystal contacts, thermal factors, or TLS parameters as an explanation for the phenomenon of intrinsic asymmetry among molecules that are in principle equivalent. Nevertheless, are all of the above determinants the cause or are they rather the effect? In the general frame of the NCS often observed in crystals of biomolecules, this paper deals with nickel(II)-substituted human carbonic anhydrase(II) (hCAII) and its SAD structure determination at the nickel edge. The structure revealed two non-equivalent molecules in the asymmetric unit, the presence of a secondary nickel-binding site at the N-terminus of both molecules (which had never been found before in the nickel-substituted enzyme) and two different coordination geometries of the active site nickel (hexa-coordinated in one molecule and mainly penta-coordinated in the other). The above-mentioned standard molecular crystallographic determinants of this asymmetry are analyzed and presented in detail for this particular case. From these considerations, we speculate on the existence of a fundamental, although yet unknown, common cause for the partial symmetry that is so often encountered in X-ray structures of biomolecules.
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Notes
The simple counting of the water molecules present in the pdb files of both structures does not seem to be a reliable parameter in the evaluation of the dehydration. In fact, the much higher resolution of our structure (1.4 Å vs 1.9 Å) greatly increases the number of water molecule characterized by a clear electron density, making this comparison devoid of significance.
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Acknowledgements
The experiments were performed on beamline ID23-1 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. We are grateful to Local Contact at the ESRF for providing assistance in using beamline ID23-1. The authors acknowledge the support and the use of resources of Instruct-ERIC, a Landmark ESFRI project, and specifically the CERM/CIRMMP Italy Centre. This work has been supported by Fondazione Cassa di Risparmio di Firenze, the European Commission (contract #675858). J.P.S. acknowledges FCT for the doctoral fellowship PD/BD/135180/2017 integrated in the Ph.D. Program in NMR applied to chemistry, materials, and biosciences.
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Silva, J.M., Giuntini, S., Cerofolini, L. et al. Non-crystallographic symmetry in proteins: Jahn–Teller-like and Butterfly-like effects?. J Biol Inorg Chem 24, 91–101 (2019). https://doi.org/10.1007/s00775-018-1630-0
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DOI: https://doi.org/10.1007/s00775-018-1630-0