› 4c8l

X-ray diffraction
1.7Å resolution

Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the artificial base pair dNaM-d5SICS at the postinsertion site (sequence context 1)

Released:
DOI: 10.2210/pdb4c8l/pdb
PDB entry 4c8l coloured by chain, front view.
PDB entry 4c8l coloured by chain, side view.
PDB entry 4c8l coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into DNA replication without hydrogen bonds.
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A
J Am Chem Soc 135 18637-43 (2013)
PMID: 24283923

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-117281 (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(*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*LHOP)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*BMNP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.06 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand GOL 5 x GOL
Ligand SO4 4 x SO4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 65.614Å b: 100.543Å c: 204.341Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.214
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

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

3 mentions without citation

Structural insights into DNA replication without hydrogen bonds.
Betz et al. (2013)
2 more