6I59

Long wavelength native-SAD phasing of Sen1 helicase

Summary for 6I59

• Entry DOI: 10.2210/pdb6i59/pdb
• Related: 5MZN
• Descriptor: Helicase SEN1, ADENOSINE-5'-DIPHOSPHATE, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: sen1 helicase, super family 1b, long-wavelength native-sad phasing, native-sad, s-sad, dna binding protein
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 1
• Total formula weight: 90372.83

Authors

Basu, S.,Olieric, V.,Matsugaki, N.,Kawano, Y.,Takashi, T.,Huang, C.Y.,Leonarski, F.,Yamada, Y.,Vera, L.,Olieric, N.,Basquin, J.,Wojdyla, J.A.,Diederichs, K.,Yamamoto, M.,Bunk, O.,Wang, M. (deposition date: 2018-11-13, release date: 2019-03-13, Last modification date: 2024-05-15)

Primary citation

Basu, S.,Olieric, V.,Leonarski, F.,Matsugaki, N.,Kawano, Y.,Takashi, T.,Huang, C.Y.,Yamada, Y.,Vera, L.,Olieric, N.,Basquin, J.,Wojdyla, J.A.,Bunk, O.,Diederichs, K.,Yamamoto, M.,Wang, M.
Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6:373-386, 2019

PubMed Abstract: Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers ( < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (TR-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

PubMed: 31098019
DOI: 10.1107/S2052252519002756

Experimental method

X-RAY DIFFRACTION (2.95 Å)