› 3eeo

X-ray diffraction
1.94Å resolution

M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.

Released:
DOI: 10.2210/pdb3eeo/pdb
PDB entry 3eeo coloured by chain, front view.
PDB entry 3eeo coloured by chain, side view.
PDB entry 3eeo coloured by chain, top view.
Source organism: Haemophilus parahaemolyticus
Entry authors: Porta JC, Christman JK, Borgstahl GEO

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116205 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II methyltransferase M.HhaI Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 37.04 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P05102 (Residues: 1-327; Coverage: 100%)
Gene name: hhaIM
Sequence domains: C-5 cytosine-specific DNA methylase
Structure domains:
5'-D(P*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Not provided
5'-D(P*DGP*DTP*DCP*DAP*DGP*(PDI)P*DGP*DCP*DAP*DTP*DGP*DG)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.55 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: R32
Unit cell:
a: 95.479Å b: 95.479Å c: 318.353Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.239 0.237 0.275
Expression systems:
  • Escherichia coli
  • Not provided

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