› 2bgw

X-ray diffraction
2.8Å resolution

XPF from Aeropyrum pernix, complex with DNA

Released:
DOI: 10.2210/pdb2bgw/pdb
Model geometry
Fit model/data
Data not deposited
PDB entry 2bgw coloured by chain, front view.
PDB entry 2bgw coloured by chain, side view.
PDB entry 2bgw coloured by chain, top view.
Source organisms:
Primary publication:
Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF, McDonald NQ
EMBO J 24 895-905 (2005)
PMID: 15719018

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115113 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Repair endonuclease XPF Chains: A, B
Molecule details ›
Chains: A, B
Length: 219 amino acids
Theoretical weight: 25.01 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9YC15 (Residues: 10-223; Coverage: 86%)
Gene name: APE_1436.1
Sequence domains:
Structure domains:
5'-D(*GP*AP*TP*CP*AP*CP*AP*GP*AP*TP *GP*CP*TP*GP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.62 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP *TP*GP*AP*TP*C)-3' Chain: D

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: P3221
Unit cell:
a: 141.312Å b: 141.312Å c: 85.311Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.223 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

18 review citations

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Yang et al. (2006)
17 more

11 mentions without citation

DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy.
McNeil et al. (2012)
10 more