› 3k5n

X-ray diffraction
3.15Å resolution

Crystal structure of E.coli Pol II-abasic DNA binary complex

Released:
DOI: 10.2210/pdb3k5n/pdb
PDB entry 3k5n coloured by chain, front view.
PDB entry 3k5n coloured by chain, side view.
PDB entry 3k5n coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural insight into translesion synthesis by DNA Pol II.
Wang F, Yang W
Cell 139 1279-89 (2009)
PMID: 20064374

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116469 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase II Chains: A, B
Molecule details ›
Chains: A, B
Length: 786 amino acids
Theoretical weight: 90.46 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P21189 (Residues: 1-783; Coverage: 100%)
Gene names: JW0059, b0060, dinA, polB
Sequence domains:
Structure domains:
DNA (5'-D(*GP*TP*CP*CP*TP*GP*(3DR)*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3') Chain: T
Molecule details ›
Chain: T
Length: 20 nucleotides
Theoretical weight: 5.99 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.01 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 88.412Å b: 147.552Å c: 96.279Å
α: 90° β: 99.98° γ: 90°
R-values:
R R work R free
0.232 0.232 0.236
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

14 review citations

Translesion DNA polymerases.
Goodman et al. (2013)
13 more

3 mentions without citation

Structural insight into translesion synthesis by DNA Pol II.
Wang et al. (2009)
2 more