› 2xo7

X-ray diffraction
2.85Å resolution

Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus

Released:
DOI: 10.2210/pdb2xo7/pdb
PDB entry 2xo7 coloured by chain, front view.
PDB entry 2xo7 coloured by chain, side view.
PDB entry 2xo7 coloured by chain, top view.
Source organisms:
Primary publication:
Chemical discrimination between dC and 5MedC via their hydroxylamine adducts.
Münzel M, Lercher L, Müller M, Carell T
Nucleic Acids Res 38 e192 (2010)
PMID: 20813757

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-115936 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 580 amino acids
Theoretical weight: 66.22 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E1C9K5 (Residues: 1-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.42 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 4 x SO4
1 modified residue:
Ligand 47C 1 x 47C

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 87.478Å b: 93.636Å c: 105.091Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.215 0.245
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

Mapping recently identified nucleotide variants in the genome and transcriptome.
Song et al. (2012)
6 more

1 mention without citation

Chemical discrimination between dC and 5MedC via their hydroxylamine adducts.
Münzel et al. (2010)