› 4f2r

X-ray diffraction
1.63Å resolution

DNA Polymerase I Large Fragment complex 3

Released:
DOI: 10.2210/pdb4f2r/pdb
PDB entry 4f2r coloured by chain, front view.
PDB entry 4f2r coloured by chain, side view.
PDB entry 4f2r coloured by chain, top view.
Source organisms:
Entry authors: Wang W, Beese LS

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-117445 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chains: A, D
Molecule details ›
Chains: A, D
Length: 592 amino acids
Theoretical weight: 67.49 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5KWC1 (Residues: 287-878; Coverage: 67%)
Gene names: GK2730, polA
Sequence domains:
Structure domains:
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.64 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.06 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand CTP 2 x CTP
Ligand MG 1 x MG
Ligand SO4 3 x SO4
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 93.22Å b: 108.48Å c: 150.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.192
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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