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)

Experimental Data Snapshot

  • Resolution: 1.4 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography

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.

(2017) IUCrJ 4: 639-647

  • DOI: 10.1107/S2052252517008557
  • Primary Citation of Related Structures:  

  • 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 vario ...

    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 de novo structural determination of biomacromolecules.

    Organizational Affiliation

    Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan.,Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
A, B
164Homo sapiensMutation(s): 0 
Gene Names: POMGNT1 (MGAT1.2)
EC: 2.4.1.-
Find proteins for Q8WZA1 (Homo sapiens)
Go to Gene View: POMGNT1
Go to UniProtKB:  Q8WZA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on MBE

Download SDF File 
Download CCD File 
A, B
C12 H15 N O8
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.4 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.210α = 90.00
b = 91.050β = 90.00
c = 53.750γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PDB_EXTRACTdata extraction
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Data collection, Database references
  • Version 1.2: 2018-01-24
    Type: Data collection