› 7omz

X-ray diffraction
1.66Å resolution

Thermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA and nicotinamide

Released:
DOI: 10.2210/pdb7omz/pdb
PDB entry 7omz coloured by chain, front view.
PDB entry 7omz coloured by chain, side view.
PDB entry 7omz coloured by chain, top view.
Source organism: Thermus sp. 2.9
Primary publication:
Molecular basis for DarT ADP-ribosylation of a DNA base.
Schuller M, Butler RE, Ariza A, Tromans-Coia C, Jankevicius G, Claridge TDW, Kendall SL, Goh S, Stewart GR, Ahel I
Nature 596 597-602 (2021)
PMID: 34408320

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100893 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA ADP-ribosyl transferase Chain: AAA
Molecule details ›
Chain: AAA
Length: 210 amino acids
Theoretical weight: 24.44 KDa
Source organism: Thermus sp. 2.9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0B0SG80 (Residues: 1-209; Coverage: 100%)
Gene names: QT17_01930, darT
Sequence domains: ssDNA thymidine ADP-ribosyltransferase, DarT
DNA (5'-D(*AP*TP*GP*TP*C)-3') Chain: AdA
Molecule details ›
Chain: AdA
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: Thermus sp. 2.9
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand NCA 1 x NCA
Ligand SCN 1 x SCN
Ligand AR6 1 x AR6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 41.963Å b: 38.89Å c: 61.179Å
α: 90° β: 101.805° γ: 90°
R-values:
R R work R free
0.153 0.151 0.18
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

The CD38 glycohydrolase and the NAD sink: implications for pathological conditions.
Zeidler et al. (2022)
4 more