› 5hnh

X-ray diffraction
1.88Å resolution

Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain

Released:
DOI: 10.2210/pdb5hnh/pdb
PDB entry 5hnh coloured by chain, front view.
PDB entry 5hnh coloured by chain, side view.
PDB entry 5hnh coloured by chain, top view.
Source organisms:
Primary publication:
Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.
Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Häner R
Nucleic Acids Res 44 7079-89 (2016)
PMID: 27422870

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107136 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Restriction endonuclease R.BpuJI Chain: A
Molecule details ›
Chain: A
Length: 288 amino acids
Theoretical weight: 33.77 KDa
Source organism: Bacillus pumilus
Expression system: Escherichia coli
UniProt:
  • Canonical: A3FMN7 (Residues: 1-285; Coverage: 62%)
Gene name: bpuJIR
Sequence domains: Restriction endonuclease BpuJI - N terminal
Structure domains:
DNA (5'-D(*GP*(YPY)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3') Chain: L
Molecule details ›
Chain: L
Length: 11 nucleotides
Theoretical weight: 3.47 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*T*(YPY)*(YPY)*C)-3') Chain: M
Molecule details ›
Chain: M
Length: 12 nucleotides
Theoretical weight: 3.82 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: SLS BEAMLINE X06DA
Spacegroup: P21212
Unit cell:
a: 59.666Å b: 164.402Å c: 44.033Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.2
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Electrochemical and Optical Biosensors for the Detection of Campylobacter and Listeria: An Update Look.
Vizzini et al. (2019)
1 other article

1 mention without citation

Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.
Probst et al. (2016)