› 4khy

X-ray diffraction
2.25Å resolution

Ternary complex of rb69 mutant L415F with ribonucleotide at -3 position

Released:
DOI: 10.2210/pdb4khy/pdb
PDB entry 4khy coloured by chain, front view.
PDB entry 4khy coloured by chain, side view.
PDB entry 4khy coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA
Proc Natl Acad Sci U S A 110 16802-7 (2013)
PMID: 24082122

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113155 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 903 amino acids
Theoretical weight: 104.69 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)-D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.55 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand TTP 1 x TTP
Ligand CA 6 x CA
Ligand NA 6 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 80.795Å b: 118.24Å c: 127.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.241
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Ribonucleotides in DNA: origins, repair and consequences.
Williams et al. (2014)
10 more

1 mention without citation

Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Clausen et al. (2013)