› 5xfc

X-ray diffraction
1.4Å resolution

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)

Released:
DOI: 10.2210/pdb5xfc/pdb
PDB entry 5xfc coloured by chain, front view.
PDB entry 5xfc coloured by chain, side view.
PDB entry 5xfc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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
IUCrJ 4 639-647 (2017)
PMID: 28989719

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186815 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 164 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8WZA1 (Residues: 92-250; Coverage: 24%)
Gene names: MGAT1.2, POMGNT1, UNQ746/PRO1475
Sequence domains: Interleukin-like EMT inducer

Ligands and Environments

1 bound ligand:
Ligand MBE 2 x MBE
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SACLA BEAMLINE BL3
Spacegroup: P21212
Unit cell:
a: 71.21Å b: 91.05Å c: 53.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.207
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals.
Zatsepin et al. (2019)
1 more

1 mention without citation

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography.
Yamashita et al. (2017)