› 3sv3

X-ray diffraction
2.1Å resolution

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP

Released:
DOI: 10.2210/pdb3sv3/pdb
PDB entry 3sv3 coloured by chain, front view.
PDB entry 3sv3 coloured by chain, side view.
PDB entry 3sv3 coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A
Nat Chem Biol 8 612-4 (2012)
PMID: 22660438

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-116902 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 60.94 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
(5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.97 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand 5SI 2 x 5SI
Ligand MG 5 x MG
Ligand GOL 4 x GOL
Ligand FMT 16 x FMT
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3121
Unit cell:
a: 108.545Å b: 108.545Å c: 90.978Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.167 0.215
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

16 review citations

The expanded genetic alphabet.
Malyshev et al. (2015)
15 more

6 mentions without citation

The expanding world of DNA and RNA.
Chen et al. (2016)
5 more