› 6nuh

X-ray diffraction
1.59Å resolution

Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog

Released:
DOI: 10.2210/pdb6nuh/pdb
PDB entry 6nuh coloured by chain, front view.
PDB entry 6nuh coloured by chain, side view.
PDB entry 6nuh coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link.
Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman BF
Nat Struct Mol Biol 26 613-618 (2019)
PMID: 31235915

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120356 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Abasic site processing protein YedK Chain: A
Molecule details ›
Chain: A
Length: 226 amino acids
Theoretical weight: 25.48 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P76318 (Residues: 2-222; Coverage: 100%)
Gene names: JW1916, b1931, yedG, yedK
Sequence domains: SOS response associated peptidase (SRAP)
DNA (5'-D(*GP*TP*CP*(PDI)P*GP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 1.99 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand BTB 1 x BTB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 47.543Å b: 44.129Å c: 55.093Å
α: 90° β: 102.34° γ: 90°
R-values:
R R work R free
0.145 0.143 0.177
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

New insights into abasic site repair and tolerance.
Thompson et al. (2020)
8 more

2 mentions without citation

Structural biology of DNA abasic site protection by SRAP proteins.
Amidon et al. (2020)
1 more