› 3bm3

X-ray diffraction
1.7Å resolution

Restriction endonuclease PspGI-substrate DNA complex

Released:
DOI: 10.2210/pdb3bm3/pdb
PDB entry 3bm3 coloured by chain, front view.
PDB entry 3bm3 coloured by chain, side view.
PDB entry 3bm3 coloured by chain, top view.
Source organism: Pyrococcus sp. GI-H
Entry authors: Szczepanowski RH, Carpenter M, Czapinska H, Tamulaitis G, Siksnys V, Bhagwat A, Bochtler M

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116097 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Restriction endonuclease type II EcoRII C-terminal domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 272 amino acids
Theoretical weight: 32.22 KDa
Source organism: Pyrococcus sp. GI-H
Expression system: Escherichia coli
UniProt:
  • Canonical: O93646 (Residues: 1-272; Coverage: 100%)
Sequence domains: EcoRII C terminal
Structure domains: Restriction Endonuclease
DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.32 KDa
Source organism: Pyrococcus sp. GI-H
Expression system: Not provided
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: Pyrococcus sp. GI-H
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CIT 1 x CIT
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P212121
Unit cell:
a: 46.884Å b: 96.06Å c: 127.069Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.192
Expression systems:
  • Escherichia coli
  • Not provided

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