› 8xe0

X-ray diffraction
2.2Å resolution

O-methyltransferase from Lycoris longituba M52W variant complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde

Released:
DOI: 10.2210/pdb8xe0/pdb
Model geometry
Fit model/data
PDB entry 8xe0 coloured by chain, front view.
PDB entry 8xe0 coloured by chain, side view.
PDB entry 8xe0 coloured by chain, top view.
Source organism: Lycoris longituba
Primary publication:
Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Hnin SYY, Nakashima Y, Kodama T, Morita H
ACS Catalysis 11865-11880 (2024)

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + norbelladine = S-adenosyl-L-homocysteine + 4'-O-methylnorbelladine
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-269457 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
norbelladine O-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 242 amino acids
Theoretical weight: 27.5 KDa
Source organism: Lycoris longituba
Expression system: Escherichia coli M15
UniProt:
  • Canonical: A0A6B9TNK2 (Residues: 1-239; Coverage: 100%)
Sequence domains: O-methyltransferase

Ligands and Environments

3 bound ligands:
Ligand H6N 1 x H6N
Ligand MG 2 x MG
Ligand SAH 2 x SAH
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Unit cell:
a: 50.421Å b: 80.862Å c: 116.597Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.203 0.233
Expression system: Escherichia coli M15

Quick links

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO