6I59 image
Deposition Date 2018-11-13
Release Date 2019-03-13
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6I59
Title:
Long wavelength native-SAD phasing of Sen1 helicase
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.95 Å
R-Value Free:
0.21
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Helicase SEN1
Gene (Uniprot):SEN1
Chain IDs:A
Chain Length:749
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Primary Citation

Abstact

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 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 (T2R-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.

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Primary Citation of related structures