› 5n0r

X-ray diffraction
1.61Å resolution

Crystal structure of OphA-DeltaC6 mutant Y66F in complex with SAM

Released:
DOI: 10.2210/pdb5n0r/pdb
PDB entry 5n0r coloured by chain, front view.
PDB entry 5n0r coloured by chain, side view.
PDB entry 5n0r coloured by chain, top view.
Source organism: Omphalotus olearius
Primary publication:
A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds.
Song H, van der Velden NS, Shiran SL, Bleiziffer P, Zach C, Sieber R, Imani AS, Krausbeck F, Aebi M, Freeman MF, Riniker S, Künzler M, Naismith JH
Sci Adv 4 eaat2720 (2018)
PMID: 30151425

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104411 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA Chain: A
Molecule details ›
Chain: A
Length: 410 amino acids
Theoretical weight: 45 KDa
Source organism: Omphalotus olearius
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A2R2JFI5 (Residues: 3-411; Coverage: 98%)
Gene name: ophMA
Sequence domains: Tetrapyrrole (Corrin/Porphyrin) Methylases

Ligands and Environments

3 bound ligands:
Ligand SAM 1 x SAM
Ligand EDO 5 x EDO
Ligand CL 2 x CL
1 modified residue:
Ligand MVA 1 x MVA

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: I222
Unit cell:
a: 86.652Å b: 93.355Å c: 165.355Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.178 0.191
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

New developments in RiPP discovery, enzymology and engineering.
Montalbán-López et al. (2021)
6 more