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T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide.

X-ray diffraction
2.3Å resolution
PDB entry 1x9w coloured by chain, front view.
PDB entry 1x9w coloured by chain, side view.
PDB entry 1x9w coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Thioredoxin 1 and DNA-directed DNA polymerase and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 35943.25 Å2
Buried surface area: 6638.84 Å2
Dissociation area: 944.11 Å2
Dissociation energy (ΔGdiss): 7.44 kcal/mol
Dissociation entropy (TΔSdiss): 11.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-114797

Macromolecules

DNA-directed DNA polymerase
Chain: A
Length: 698 amino acids
Theoretical weight: 79.09 KDa
Source organism: Escherichia phage T7
Expression system: Escherichia coli
UniProt:
  • Canonical: P00581 (Residues: 1-704; Coverage: 99%)
Gene name: 5
Pfam: DNA polymerase family A
InterPro:
CATH:
SCOP:
DNA-directed DNA polymerase in PDB entry 1x9w, assembly 1, front view.
DNA-directed DNA polymerase in PDB entry 1x9w, assembly 1, side view.
DNA-directed DNA polymerase in PDB entry 1x9w, assembly 1, top view.
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Thioredoxin 1
Chain: B
Length: 108 amino acids
Theoretical weight: 11.69 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AA25 (Residues: 2-109; Coverage: 99%)
Gene names: JW5856, b3781, fipA, trxA, tsnC
Pfam: Thioredoxin
InterPro:
CATH: Glutaredoxin
SCOP: Thioltransferase
Thioredoxin 1 in PDB entry 1x9w, assembly 1, front view.
Thioredoxin 1 in PDB entry 1x9w, assembly 1, side view.
Thioredoxin 1 in PDB entry 1x9w, assembly 1, top view.
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DNA chain C
Name: 5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*GP*AP*(2DT))-3'
Representative chains: C
Length: 22 nucleotides
Theoretical weight: 6.93 KDa
5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' in PDB entry 1x9w, assembly 1, front view.
5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' in PDB entry 1x9w, assembly 1, side view.
5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' in PDB entry 1x9w, assembly 1, top view.
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DNA chain D
Name: 5'-D(*CP*CP*CP*(AFG)*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3'
Representative chains: D
Length: 26 nucleotides
Theoretical weight: 7.94 KDa
5'-D(*CP*CP*CP*(AFG)*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3' in PDB entry 1x9w, assembly 1, front view.
5'-D(*CP*CP*CP*(AFG)*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3' in PDB entry 1x9w, assembly 1, side view.
5'-D(*CP*CP*CP*(AFG)*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3' in PDB entry 1x9w, assembly 1, top view.
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