5XFD

Serial femtosecond X-ray structure of Agrocybe cylindracea galectin with lactose solved by Se-SAD using XFEL (refined against 60,000 patterns)

5XFD の概要

• エントリーDOI: 10.2210/pdb5xfd/pdb
• 関連するPDBエントリー: 5XFC
• 関連するBIRD辞書のPRD_ID: PRD_900133
• 分子名称: Galactoside-binding lectin, alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose (3 entities in total)
• 機能のキーワード: sugar binding protein
• 由来する生物種: Agrocybe cylindracea
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 39754.95

構造登録者

Kuwabara, N.,Fumiaki, Y.,Kato, R. (登録日: 2017-04-10, 公開日: 2017-08-30, 最終更新日: 2024-10-30)

主引用文献

Yamashita, K.,Kuwabara, N.,Nakane, T.,Murai, T.,Mizohata, E.,Sugahara, M.,Pan, D.,Masuda, T.,Suzuki, M.,Sato, T.,Kodan, A.,Yamaguchi, T.,Nango, E.,Tanaka, T.,Tono, K.,Joti, Y.,Kameshima, T.,Hatsui, T.,Yabashi, M.,Manya, H.,Endo, T.,Kato, R.,Senda, T.,Kato, H.,Iwata, S.,Ago, H.,Yamamoto, M.,Yumoto, F.,Nakatsu, T.
Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
IUCrJ, 4:639-647, 2017

PubMed Abstract: Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine structural determination of biomacromolecules.

PubMed: 28989719
DOI: 10.1107/S2052252517008557

実験手法

X-RAY DIFFRACTION (1.5 Å)