› 4fzy

X-ray diffraction
2.5Å resolution

Exonuclease X in complex with 12bp blunt-ended dsDNA

Released:
DOI: 10.2210/pdb4fzy/pdb
PDB entry 4fzy coloured by chain, front view.
PDB entry 4fzy coloured by chain, side view.
PDB entry 4fzy coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease.
Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T
Nucleic Acids Res 41 7556-65 (2013)
PMID: 23771145

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117519 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Exodeoxyribonuclease 10 Chains: A, B
Molecule details ›
Chains: A, B
Length: 175 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEK0 (Residues: 1-167; Coverage: 76%)
Gene names: JW1833, b1844, exoX, yobC
Sequence domains: Exonuclease
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*TP*GP*TP*AP*GP*AP*TP*TP*CP*GP*AP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.72 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(P*CP*TP*CP*GP*AP*AP*TP*CP*TP*AP*CP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.61 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 4 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 37.282Å b: 78.887Å c: 146.668Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.219 0.241
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 citation in other articles

Internal RNA 2'O-methylation in the HIV-1 genome counteracts ISG20 nuclease-mediated antiviral effect.
El Kazzi et al. (2023)
3 more

2 mentions without citation

Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease.
Wang et al. (2013)
1 more