› 4fzx

X-ray diffraction
2.3Å resolution

Exonuclease X in complex with 3' overhanging duplex DNA

Released:
DOI: 10.2210/pdb4fzx/pdb
PDB entry 4fzx coloured by chain, front view.
PDB entry 4fzx coloured by chain, side view.
PDB entry 4fzx 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-117518 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Exodeoxyribonuclease 10 Chains: C, D
Molecule details ›
Chains: C, D
Length: 175 amino acids
Theoretical weight: 20.49 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(P*GP*TP*CP*AP*TP*TP*GP*TP*GP*GP*AP*TP*CP*CP*GP*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 17 nucleotides
Theoretical weight: 5.26 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(P*CP*GP*GP*AP*TP*CP*CP*AP*CP*AP*AP*TP*GP*AP*CP*CP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 17 nucleotides
Theoretical weight: 5.16 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 4 x NA
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 33.475Å b: 107.927Å c: 117.124Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 citation in other articles

DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.
Zhitnikova et al. (2017)
2 more

3 mentions without citation

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