5XFC

Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)

Summary for 5XFC

• Entry DOI: 10.2210/pdb5xfc/pdb
• Related: 5XFD
• Descriptor: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, 4-nitrophenyl beta-D-mannopyranoside (3 entities in total)
• Functional Keywords: glycosyltransferase, carbohydrate-binding domain, sugar binding protein
• Biological source: Homo sapiens (Human)
• Cellular location: Golgi apparatus membrane ; Single-pass type II membrane protein : Q8WZA1
• Total number of polymer chains: 2
• Total formula weight: 36129.91

Authors

Kuwabara, N.,Fumiaki, Y.,Kato, R.,Manya, H. (deposition date: 2017-04-10, release date: 2017-08-30, Last modification date: 2024-11-06)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.4 Å)