› 5dwa

X-ray diffraction
1.5Å resolution

Crystal structure of pre-specific restriction endonuclease AgeI-DNA complex

Released:
DOI: 10.2210/pdb5dwa/pdb
PDB entry 5dwa coloured by chain, front view.
PDB entry 5dwa coloured by chain, side view.
PDB entry 5dwa coloured by chain, top view.
Source organisms:
Primary publication:
Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.
Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V
Nucleic Acids Res 45 3547-3558 (2017)
PMID: 28039325

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118595 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II restriction enzyme AgeI Chains: A, B
Molecule details ›
Chains: A, B
Length: 278 amino acids
Theoretical weight: 30.58 KDa
Source organism: Thalassobius gelatinovorus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KHV6 (Residues: 1-278; Coverage: 100%)
Gene name: ageIR
Sequence domains: BsaWI restriction endonuclease type 2
DNA (5'-D(*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*G*)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X12, RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 66.003Å b: 79.806Å c: 101.655Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.152 0.185
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 citation in other articles

Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate.
McMahon et al. (2020)
5 more

1 mention without citation

Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.
Tamulaitiene et al. (2017)