› 3ssd

X-ray diffraction
2.2Å resolution

DNA binding domain of restriction endonuclease bound to DNA

Released:
DOI: 10.2210/pdb3ssd/pdb
PDB entry 3ssd coloured by chain, front view.
PDB entry 3ssd coloured by chain, side view.
PDB entry 3ssd coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.
Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V
Nucleic Acids Res 40 7552-62 (2012)
PMID: 22570415

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116895 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type IV methyl-directed restriction enzyme EcoKMcrB subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 170 amino acids
Theoretical weight: 19.66 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P15005 (Residues: 1-161; Coverage: 35%)
Gene names: JW5871, b4346, mcrB, rglB
Sequence domains: MrcB-like, N-terminal domain
Structure domains: Metal Transport, Frataxin; Chain A
DNA (5'-D(*T*GP*AP*GP*AP*(5CM)P*CP*GP*GP*TP*AP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P212121
Unit cell:
a: 36.085Å b: 67.189Å c: 142.414Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.196 0.262
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

The other face of restriction: modification-dependent enzymes.
Loenen et al. (2014)
3 more

2 mentions without citation

The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.
Sukackaite et al. (2012)
1 more