› 4jrp

X-ray diffraction
1.95Å resolution

Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide

Released:
DOI: 10.2210/pdb4jrp/pdb
PDB entry 4jrp coloured by chain, front view.
PDB entry 4jrp coloured by chain, side view.
PDB entry 4jrp coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.
Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE
Nucleic Acids Res 41 5887-97 (2013)
PMID: 23609540

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117705 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Exodeoxyribonuclease I Chains: A, B
Molecule details ›
Chains: A, B
Length: 478 amino acids
Theoretical weight: 54.85 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P04995 (Residues: 1-475; Coverage: 100%)
Gene names: JW1993, b2011, cpeA, sbcB, xonA
Sequence domains:
Structure domains:
5cy-dT13 Chains: C, D
Molecule details ›
Chains: C, D
Length: 14 nucleotides
Theoretical weight: 4.36 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand SO4 14 x SO4
Ligand GOL 2 x GOL
Ligand IPA 1 x IPA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P43
Unit cell:
a: 91.3Å b: 91.3Å c: 159.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.213 0.259
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

2 review citations

Processivity in Bacterial Glycosyltransferases.
Yakovlieva et al. (2020)
1 more

5 mentions without citation

Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins.
Shen et al. (2016)
4 more