› 8ka5

X-ray diffraction
2.8Å resolution

Arabidopsis AP endonuclease ARP complex with 20bp THF-containing DNA

Released:
DOI: 10.2210/pdb8ka5/pdb
PDB entry 8ka5 coloured by chain, front view.
PDB entry 8ka5 coloured by chain, side view.
PDB entry 8ka5 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the catalytic mechanism of the AP endonuclease AtARP.
Guo W, Wu W, Wen Y, Gao Y, Zhuang S, Meng C, Chen H, Zhao Z, Hu K, Wu B
Structure (2024)
PMID: 38503293

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-240144 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 33.7 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P45951 (Residues: 240-536; Coverage: 55%)
Gene names: ARP, At2g41460, REF, T26J13.5
Sequence domains: Endonuclease/Exonuclease/phosphatase family
DNA (43-MER) Chains: B, C, D
Molecule details ›
Chains: B, C, D
Length: 43 nucleotides
Theoretical weight: 13.26 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand 3DR 1 x 3DR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P3221
Unit cell:
a: 72.093Å b: 72.093Å c: 188.189Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.201 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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