› 4dle

X-ray diffraction
2.44Å resolution

Ternary Structure of the large Fragment of Taq DNA Polymerase: 4-Fluoroproline Variant

Released:
DOI: 10.2210/pdb4dle/pdb
PDB entry 4dle coloured by chain, front view.
PDB entry 4dle coloured by chain, side view.
PDB entry 4dle coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of protein
Holzberger B, Obeid S, Welte W, Diederichs K, Marx A
Chem Sci 3 2924-2931 (2012)

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-117329 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 61.51 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
DNA primer Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
DNA template Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand GOL 2 x GOL
Ligand DCT 1 x DCT
Ligand MN 1 x MN
Ligand EDO 1 x EDO
2 modified residues:
Ligand FP9 32 x FP9
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P3121
Unit cell:
a: 109.619Å b: 109.619Å c: 91.011Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.235 0.233 0.282
Expression systems:
  • Escherichia coli
  • Not provided

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