addenda and errata\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL BIOLOGY
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ISSN: 2053-230X
Volume 72| Part 3| March 2016| Pages 253-254

Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO

aSchool of Chemistry, Faculty of Engineering and Physical Sciences, University of Manchester, Brunswick Street, Manchester M13 9PL, England, and bCrystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
*Correspondence e-mail: john.helliwell@manchester.ac.uk

Edited by N. Sträter, University of Leipzig, Germany (Received 12 October 2015; accepted 15 January 2016; online 19 February 2016)

A re-refinement of 4g4a , the room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO is published as an addendum to Tanley et al. [(2012), Acta Cryst. F68, 1300–1306] . This example illustrates the benefits of sharing raw diffraction images, as well as structure factors and molecular coordinates, as the diffraction resolution of the study is now much improved at 1.70 Å.

We have re-refined our previously published room temperature crystal structure of cisplatin binding to hen egg lysozyme (PDB entry 4g4a ; Tanley et al., 2012[Tanley, S. W. M., Schreurs, A. M. M., Kroon-Batenburg, L. M. J. & Helliwell, J. R. (2012). Acta Cryst. F68, 1300-1306.]) at a resolution of 1.7 Å. This structure was originally refined by us at 2.4 Å resolution and subsequently re-refined by Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]) to 2.0 Å resolution. Both studies extended the diffraction resolution by reprocessing subsets of the same data set's raw diffraction images [originally held at Utrecht University; Tanley et al. (2013[Tanley, S. W. M., Schreurs, A. M. M., Helliwell, J. R. & Kroon-Batenburg, L. M. J. (2013). J. Appl. Cryst. 46, 108-119.]) and which are now accessible at the University of Manchester (Tanley & Helliwell, 2015[Tanley, S. W. M. & Helliwell, J. R. (2015). https://www.escholar.manchester.ac.uk/uk-ac-man-scw:215887. doi: 10.15127/1.215887.])]. Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]) (PDB code 4yen ) interpreted the platinum coordination spheres as [PtCl3His15] for the platinum ion (Ptδ) coordinated to Nδ of His15 and [PtCl2His15Arg14] for the second platinum ion (Pt) bound to His15-N. A re-refinement of 4g4a at the extended resolution of 1.7 Å presented here gives improved clarity, and a small spread of B factors, of the Pt ligand assignments which are [PtClNH3NH3His15] for Ptδ, and [PtClNH3His15Arg14] for Pt; see Fig. 1[link]. Details are provided in the Supporting Information.

[Figure 1]
Figure 1
Stereo image of the cisplatin coordination to His15. A platinum ion is bound to both the Nδ and N sides of the imidazole ring with ligands (two ammines and one Cl atom at Ptδ, and one chlorine, one ammine and the Arg14 side chain at Pt). Electron-density maps: 2FoFc (in blue at 1.0 r.m.s.), FoFc (in green at 5.0σ) and anomalous difference Fourier map (in orange at 3.0σ) of the final model. The two platinum ions are depicted in purple, the Cl atoms in brown, the N atoms in blue, O atoms in red and H atoms in charcoal grey. The orientation of each ammine's three H atoms and of the Arg14 side-chain H atoms at 1.7 Å diffraction resolution are obviously approximate (the Arg14 side-chain nitrogen closest to the Pt in particular would present a lone pair of electrons to the metal atom). This figure was prepared using CCP4mg (McNicholas et al., 2011[McNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. (2011). Acta Cryst. D67, 386-394.]).

The following references are cited in the Supporting Information for this article: Afonine et al. (2012[Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352-367.]); Casini et al. (2007[Casini, A., Mastrobuoni, G., Temperini, C., Gabbiani, C., Francese, S., Moneti, G., Supuran, C. T., Scozzafava, A. & Messori, L. (2007). Chem. Commun. 156-158.]); Diederichs & Karplus (2013[Diederichs, K. & Karplus, P. A. (2013). Acta Cryst. D69, 1215-1222.]); Joosten et al. (2014[Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. (2014). IUCrJ, 1, 213-220.]); Murshudov et al. (1997[Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.]); Schreurs et al. (2010[Schreurs, A. M. M., Xian, X. & Kroon-Batenburg, L. M. J. (2010). J. Appl. Cryst. 43, 70-82.]); Tanley, Schreurs, Kroon-Batenburg, Meredith et al. (2012[Tanley, S. W. M., Schreurs, A. M. M., Kroon-Batenburg, L. M. J., Meredith, J., Prendergast, R., Walsh, D., Bryant, P., Levy, C. & Helliwell, J. R. (2012). Acta Cryst. D68, 601-612.]); Tanley et al. (2015[Tanley, S. W. M. , Diederichs, K., Kroon- Batenburg, L. M. J. , Levy, C., Schreurs, A. M. M. & Helliwell, J. R. (2015). Acta Cryst. D71, 1982-1983.]).

Supporting information


Acknowledgements

We thank Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]) for their valuable critique and to which we responded (Tanley et al., 2015[Tanley, S. W. M. , Diederichs, K., Kroon- Batenburg, L. M. J. , Levy, C., Schreurs, A. M. M. & Helliwell, J. R. (2015). Acta Cryst. D71, 1982-1983.]). SWMT was funded under an EPSRC PhD Research Studentship at the School of Chemistry, University of Manchester.

References

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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoSTRUCTURAL BIOLOGY
COMMUNICATIONS
ISSN: 2053-230X
Volume 72| Part 3| March 2016| Pages 253-254
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