› 6fbh

X-ray diffraction
1.8Å resolution

KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the sixth primer nucleotide.

Released:
DOI: 10.2210/pdb6fbh/pdb
PDB entry 6fbh coloured by chain, front view.
PDB entry 6fbh coloured by chain, side view.
PDB entry 6fbh coloured by chain, top view.
Source organisms:
Primary publication:
Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Kropp HM, Dürr SL, Peter C, Diederichs K, Marx A
Proc Natl Acad Sci U S A 115 9992-9997 (2018)
PMID: 30224478

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-119896 (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: 541 amino acids
Theoretical weight: 61.07 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*CP*CP*CP*AP*(OH3)P*CP*GP*GP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*GP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.94 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 2 x MN
Ligand EDO 1 x EDO
Ligand XG4 1 x XG4
1 modified residue:
Ligand D4B 1 x D4B

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3121
Unit cell:
a: 109.706Å b: 109.706Å c: 91.292Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.196 0.223
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Building better polymerases: Engineering the replication of expanded genetic alphabets.
Ouaray et al. (2020)
2 more