› 1d9d

X-ray diffraction
2.18Å resolution

CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3'

Released:
DOI: 10.2210/pdb1d9d/pdb
PDB entry 1d9d coloured by chain, front view.
PDB entry 1d9d coloured by chain, side view.
PDB entry 1d9d coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural origins of the exonuclease resistance of a zwitterionic RNA.
Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M
Proc Natl Acad Sci U S A 96 14240-5 (1999)
PMID: 10588690

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113056 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (2 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 605 amino acids
Theoretical weight: 68.19 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00582 (Residues: 324-928; Coverage: 65%)
Gene names: JW3835, b3863, polA, resA
Sequence domains:
Structure domains:
5'-D(*TP*CP*GP)-R(AP*(U31)P*(C31))-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.92 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 1 x MG
Ligand SO4 4 x SO4
2 modified residues:
Ligand U31 1 x U31
Ligand C31 1 x C31

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P43
Unit cell:
a: 102.55Å b: 102.55Å c: 86.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.238
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Antisense oligonucleotides in therapy for neurodegenerative disorders.
Evers et al. (2015)
6 more

4 mentions without citation

DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.
Tuszynska et al. (2011)
3 more