Controlled beam divergence on a laboratory diffractometer to improve spatial resolution of reflections for Era protein crystals from Staphylococcus aureus
https://doi.org/10.26907/2542-064X.2025.2.268-275
Abstract
Obtaining spatial structures with high resolution by the XRD method is still associated with significant difficulties for laboratory single-crystal diffractometers incorporating modern confocal multilayer optics with high intensity and small X-ray beam diameter (≤ 100 μm). As the unit cell size increases, the distance between reflections in the diffraction pattern decreases, which leads to their overlapping. To minimize the overlap and separate reflections as distinct peaks, the distance from the crystal to the detector is traditionally increased. However, this approach is not always successful due to the divergence of the X-ray beam. A potential alternative solution is to optimize the beam divergence parameters in the optical device of the X-ray source. Using an Era protein crystal from Staphylococcus aureus with large unit cell parameters (a = b = 78.1(1) Å and c = 244.9(2) Å), a successful optimization of the X-ray beam divergence parameter selection for high-resolution XRD data acquisition was demonstrated.
About the Authors
D. R. IslamovRussian Federation
Daut R. Islamov - Cand. Sci. (Chemistry), Senior Researcher, Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology.
Kazan
Competing Interests:
The authors declare no conflicts of interest
A. D. Biktimirov
Russian Federation
Artem D. Biktimirov - Laboratory Research Assistant, Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology.
Kazan
Competing Interests:
The authors declare no conflicts of interest
E. A. Klochkova
Russian Federation
Evelina A. Klochkova - Senior Researcher, Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology.
Kazan
Competing Interests:
The authors declare no conflicts of interest
K. S. Usachev
Russian Federation
Konstantin S. Usachev - Dr. Sci. (Physics and Mathematics), Leading Researcher, Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan FU; Deputy Head of Center for Integrative Structural Biology, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center “Kurchatov Institute”.
Kazan, Moscow
Competing Interests:
The authors declare no conflicts of interest
References
1. Meulenbroek E., Pannu N. Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Cockayne syndrome protein A in complex with DNA damage-binding protein 1. Acta Crystallogr., Sect. F: Struct. Biol. Commun., 2012, vol. F68, pt. 1, pp. 45–48. https://doi.org/10.1107/S1744309111045842.
2. Timofeev V., Samygina V. Protein crystallography: Achievements and challenges. Crystals, 2023, vol. 13, no. 1, art. 71. https://doi.org/10.3390/cryst13010071.
3. Goyal A., Muthu K., Panneerselvam M., Pole A.K., Ramadas K. Molecular dynamics simulation of the Staphylococcus aureus YsxC protein: Molecular insights into ribosome assembly and allosteric inhibition of the protein. J. Mol. Model., 2011, vol. 17, no. 12, pp. 3129–3149. https://doi.org/10.1007/s00894-011-0998-3.
4. Sayed A., Matsuyama S., Inouye M. Era, an essential Escherichia coli small G-protein, binds to the 30S ribosomal subunit. Biochem. Biophys. Res. Commun., 1999, vol. 264, no. 1 pp. 51–54. https://doi.org/10.1006/bbrc.1999.1471.
5. Inoue K., Alsina J., Chen J.Q., Inouye M. Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli. Mol. Microbiol., 2003, vol. 48, no. 4, pp. 1005–1016. https://doi.org/10.1046/j.1365-2958.2003.03475.x.
6. Bunner A.E., Nord S., Wikstrӧm P.M., Williamson J.R. The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution. J. Mol. Biol., 2010, vol. 398, no. 1, pp. 1–7. https://doi.org/10.1016/j.jmb.2010.02.036.
7. Stijn Blot R.N., Vandewoude K., Colardyn F. Staphylococcus aureus infections. N. Engl. J. Med., 1998. vol. 339, no. 27, pp. 2025–2026. https://doi.org/10.1056/nejm199812313392716.
8. Jeljaszewicz J., Mlynarczyk G., Mlynarczyk A. Antibiotic resistance in Gram-positive cocci. Int. J. Antimicrob. Agents, 2000, vol. 16, no. 4, pp. 473–478. https://doi.org/10.1016/s0924-8579(00)00289-2.
9. Fierobe L., Decré D., Mùller C., Lucet J.-C., Marmuse J.-P., Mantz J., Desmonts J.-M. Methicillin-resistant Staphylococcus aureus as a causative agent of postoperative intra-abdominal infection: Relation to nasal colonization. Clin. Infect. Dis., 1999, vol. 29, no. 5, pp. 1231–1238. https://doi.org/10.1086/313454.
10. Klochkova E.A., Islamov D.R., Biktimirov A.D., Rogachev A.V., Validov Sh.Z., Bikmullin A.G., Simakin A.V., Peters G.S., Yusupov M.M., Usachev K.S. Extraction, purification, and crystallization of GTPase Era from Staphylococcus aureus. Crystallogr. Rep., 2023, vol. 68, no. 2, pp. 288–292. https://doi.org/10.1134/S1063774523010133.
11. Agilent. CrysAlis PRO. Agilent Technologies Ltd, Yarnton, Oxfordshire, England. 2014.
12. Chen X., Court D.L., Ji X. Crystal structure of ERA: A GTPase-dependent cell cycle regulator containing an RNA binding motif. PNAS, 1999. vol. 15, no. 96, pp. 8396–8401. https://doi.org/10.1073/pnas.96.15.8396.
Review
For citations:
Islamov D.R., Biktimirov A.D., Klochkova E.A., Usachev K.S. Controlled beam divergence on a laboratory diffractometer to improve spatial resolution of reflections for Era protein crystals from Staphylococcus aureus. Uchenye Zapiski Kazanskogo Universiteta Seriya Estestvennye Nauki. 2025;167(2):268-275. (In Russ.) https://doi.org/10.26907/2542-064X.2025.2.268-275