› 4f4k

X-ray diffraction
1.6Å resolution

DNA Polymerase I Large Fragment Complex 6

Released:
DOI: 10.2210/pdb4f4k/pdb
PDB entry 4f4k coloured by chain, front view.
PDB entry 4f4k coloured by chain, side view.
PDB entry 4f4k 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-117453 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 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: DNA polymerase family A
Structure domains:
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.68 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SO4 3 x SO4
Ligand DG3 1 x DG3
Ligand MN 1 x MN
Ligand MPD 1 x MPD
1 modified residue:
Ligand DDG 2 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 93.81Å b: 109.22Å c: 150.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.194
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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