› 5dnk

X-ray diffraction
1.9Å resolution

The structure of PKMT1 from Rickettsia prowazekii in complex with AdoHcy

Released:
DOI: 10.2210/pdb5dnk/pdb
PDB entry 5dnk coloured by chain, front view.
PDB entry 5dnk coloured by chain, side view.
PDB entry 5dnk coloured by chain, top view.
Source organism: Rickettsia prowazekii str. Madrid E
Primary publication:
Structural Insights into Substrate Recognition and Catalysis in Outer Membrane Protein B (OmpB) by Protein-lysine Methyltransferases from Rickettsia.
Abeykoon AH, Noinaj N, Choi BE, Wise L, He Y, Chao CC, Wang G, Gucek M, Ching WM, Chock PB, Buchanan SK, Yang DC
J Biol Chem 291 19962-74 (2016)
PMID: 27474738

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126505 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
protein lysine methyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 554 amino acids
Theoretical weight: 63.48 KDa
Source organism: Rickettsia prowazekii str. Madrid E
Expression system: Escherichia coli
UniProt:
  • Canonical: O05979 (Residues: 1-553; Coverage: 100%)
Gene name: RP789
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand SAH 2 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 98.016Å b: 62.127Å c: 107.392Å
α: 90° β: 100.88° γ: 90°
R-values:
R R work R free
0.203 0.202 0.249
Expression system: Escherichia coli

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Citations

3 review citations

The enigmatic biology of rickettsiae: recent advances, open questions and outlook.
McGinn et al. (2021)
2 more

2 mentions without citation

Structural Insights into Substrate Recognition and Catalysis in Outer Membrane Protein B (OmpB) by Protein-lysine Methyltransferases from Rickettsia.
Abeykoon et al. (2016)
1 more