› 4ez9

X-ray diffraction
1.64Å resolution

Bacillus DNA Polymerase I Large Fragment Complex 2

Released:
DOI: 10.2210/pdb4ez9/pdb
PDB entry 4ez9 coloured by chain, front view.
PDB entry 4ez9 coloured by chain, side view.
PDB entry 4ez9 coloured by chain, top view.
Source organism: Geobacillus kaustophilus HTA426
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-117442 (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*(2DT))-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.65 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand MPD 1 x MPD
Ligand D3T 1 x D3T
1 modified residue:
Ligand 2DT 2 x 2DT

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 93.92Å b: 108.96Å c: 149.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.168 0.191
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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