› 2okc

X-ray diffraction
2.2Å resolution

Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

Released:
DOI: 10.2210/pdb2okc/pdb
PDB entry 2okc coloured by chain, front view.
PDB entry 2okc coloured by chain, side view.
PDB entry 2okc coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Entry author: Joint Center for Structural Genomics (JCSG)

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183576 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type I restriction enzyme BthVORF4518P methylase subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 445 amino acids
Theoretical weight: 50.66 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli
UniProt:
  • Canonical: Q89Z59 (Residues: 1-444; Coverage: 94%)
Gene names: BT_4518, hsdM
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAM 2 x SAM
3 bound ligands:
Ligand GOL 1 x GOL
Ligand IPA 2 x IPA
Ligand CL 1 x CL
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P212121
Unit cell:
a: 75.44Å b: 85.85Å c: 152.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.182 0.232
Expression system: Escherichia coli

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