› 4ds5

X-ray diffraction
1.68Å resolution

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+

Released:
DOI: 10.2210/pdb4ds5/pdb
PDB entry 4ds5 coloured by chain, front view.
PDB entry 4ds5 coloured by chain, side view.
PDB entry 4ds5 coloured by chain, top view.
Source organism: Geobacillus kaustophilus HTA426
Primary publication:
Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
Wang W, Wu EY, Hellinga HW, Beese LS
J Biol Chem 287 28215-26 (2012)
PMID: 22648417

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-117344 (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: 592 amino acids
Theoretical weight: 67.47 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5KWC1 (Residues: 287-878; Coverage: 67%)
Gene names: GK2730, polA
Sequence domains: DNA polymerase family A
Structure domains:
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.65 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.06 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 93.88Å b: 108.86Å c: 150.96Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.199
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.
Wei et al. (2016)
7 more

3 mentions without citation

Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates.
Pugliese et al. (2017)
2 more