› 1l3s

X-ray diffraction
1.7Å resolution

Crystal Structure of Bacillus DNA Polymerase I Fragment complexed to 9 base pairs of duplex DNA.

Released:
DOI: 10.2210/pdb1l3s/pdb
PDB entry 1l3s coloured by chain, front view.
PDB entry 1l3s coloured by chain, side view.
PDB entry 1l3s coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
Johnson SJ, Taylor JS, Beese LS
Proc Natl Acad Sci U S A 100 3895-900 (2003)
PMID: 12649320

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 domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114112 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 580 amino acids
Theoretical weight: 66.17 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P52026 (Residues: 297-876; Coverage: 66%)
Gene names: pol, polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.92 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
2 bound ligands:
Ligand SO4 5 x SO4
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200, NSLS BEAMLINE X12B
Spacegroup: P212121
Unit cell:
a: 86.289Å b: 93.254Å c: 106.292Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

37 review citations

Structure-function relationships among RNA-dependent RNA polymerases.
Ng et al. (2008)
36 more

23 mentions without citation

E pluribus unum, no more: from one crystal, many conformations.
Woldeyes et al. (2014)
22 more