› 4c8k

X-ray diffraction
2.17Å resolution

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP

Released:
DOI: 10.2210/pdb4c8k/pdb
PDB entry 4c8k coloured by chain, front view.
PDB entry 4c8k coloured by chain, side view.
PDB entry 4c8k 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-117280 (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*C*DOC)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand GOL 2 x GOL
Ligand BMR 1 x BMR
Ligand MG 2 x MG
Ligand TRS 1 x TRS
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: 115.039Å b: 115.039Å c: 91.106Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.181 0.221
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

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