› 8yjn

X-ray diffraction
2.42Å resolution

Structure of E. coli glycyl radical enzyme YbiW with bound glycerol

Released:
DOI: 10.2210/pdb8yjn/pdb
PDB entry 8yjn coloured by chain, front view.
PDB entry 8yjn coloured by chain, side view.
PDB entry 8yjn coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
A Widespread Radical-Mediated Glycolysis Pathway.
Ma K, Xue B, Chu R, Zheng Y, Sharma S, Jiang L, Hu M, Xie Y, Hu Y, Tao T, Zhou Y, Liu D, Li Z, Yang Q, Chen Y, Wu S, Tong Y, Robinson RC, Yew WS, Jin X, Liu Y, Zhao H, Ang EL, Wei Y, Zhang Y
J Am Chem Soc (2024)
PMID: 39283600

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-252044 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable dehydratase YbiW Chain: A
Molecule details ›
Chain: A
Length: 826 amino acids
Theoretical weight: 91.75 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P75793 (Residues: 1-810; Coverage: 100%)
Gene names: JW0807, b0823, ybiW
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: F222
Unit cell:
a: 114.926Å b: 207.04Å c: 210.555Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.213
Expression system: Escherichia coli BL21(DE3)

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