› 5edw

X-ray diffraction
2.62Å resolution

Ternary structure of Dpo4 bound to G in the template base paired with incoming dTTP

Released:
DOI: 10.2210/pdb5edw/pdb
PDB entry 5edw coloured by chain, front view.
PDB entry 5edw coloured by chain, side view.
PDB entry 5edw coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Entry authors: Koag M-C, Lee S

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118626 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 39.02 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 19 nucleotides
Theoretical weight: 5.7 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand TTP 1 x TTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P21212
Unit cell:
a: 98.516Å b: 101.994Å c: 52.864Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.284
Expression systems:
  • Escherichia coli
  • Not provided

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