› 6vnp

X-ray diffraction
2.42Å resolution

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT

Released:
DOI: 10.2210/pdb6vnp/pdb
PDB entry 6vnp coloured by chain, front view.
PDB entry 6vnp coloured by chain, side view.
PDB entry 6vnp coloured by chain, top view.
Source organisms:
Entry authors: Jung H, 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-120780 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 341 amino acids
Theoretical weight: 39.02 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3') Chains: B, E, H, P
Molecule details ›
Chains: B, E, H, P
Length: 14 nucleotides
Theoretical weight: 4.4 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chains: C, F, I, T
Molecule details ›
Chains: C, F, I, T
Length: 19 nucleotides
Theoretical weight: 5.69 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DZ4 4 x DZ4
Ligand MG 8 x MG
1 modified residue:
Ligand A38 4 x A38

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P1
Unit cell:
a: 53.255Å b: 98.984Å c: 102.875Å
α: 90.03° β: 89.99° γ: 89.92°
R-values:
R R work R free
0.199 0.199 0.242
Expression systems:
  • Escherichia coli
  • Not provided

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