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X-ray diffraction
2.67Å resolution

Bst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-amino primer, dGTP, and calcium time-resolved 1h

Released:
DOI: 10.2210/pdb8sci/pdb
PDB entry 8sci coloured by chain, front view.
PDB entry 8sci coloured by chain, side view.
PDB entry 8sci coloured by chain, top view.
Source organisms:
Primary publication:
Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity.
Lelyveld VS, Fang Z, Szostak JW
Science 382 423-429 (2023)
PMID: 37883544

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-232632 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chains: A, D
Molecule details ›
Chains: A, D
Length: 579 amino acids
Theoretical weight: 66.07 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: D9N168 (Residues: 1-579; Coverage: 100%)
Gene names: DPO1, polA
Sequence domains:
DNA primer/product Chains: B, E
Molecule details ›
Chains: B, E
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA template Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand DPO 2 x DPO
Ligand DGT 2 x DGT
Ligand CA 2 x CA
Ligand SO4 1 x SO4
1 modified residue:
Ligand C42 2 x C42

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 93.163Å b: 108.541Å c: 148.783Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.184 0.256
Expression systems:
  • Escherichia coli
  • Not provided

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