6I5C image
Deposition Date 2018-11-13
Release Date 2019-03-13
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6I5C
Title:
Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex
Biological Source:
Source Organism:
Bos taurus (Taxon ID: 9913)
Rattus norvegicus (Taxon ID: 10116)
Gallus gallus (Taxon ID: 9031)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.95 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin alpha-1B chain
Chain IDs:A, C
Chain Length:440
Number of Molecules:2
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin beta-2B chain
Gene (Uniprot):TUBB2B
Chain IDs:B, D
Chain Length:431
Number of Molecules:2
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Stathmin-4
Gene (Uniprot):Stmn4
Chain IDs:E
Chain Length:136
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:TUBULIN-TYROSINE LIGASE
Chain IDs:F
Chain Length:379
Number of Molecules:1
Biological Source:Gallus gallus
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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Disease

Primary Citation of related structures