› 6nhx

X-ray diffraction
1.4Å resolution

mycobacterial DNA ligase D complexed with ATP and MES

Released:
DOI: 10.2210/pdb6nhx/pdb
PDB entry 6nhx coloured by chain, front view.
PDB entry 6nhx coloured by chain, side view.
PDB entry 6nhx coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.
Unciuleac MC, Goldgur Y, Shuman S
J Biol Chem 294 5094-5104 (2019)
PMID: 30718283

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167130 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ATP-dependent DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 307 amino acids
Theoretical weight: 34.08 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 41.089Å b: 49.687Å c: 73.522Å
α: 90° β: 103.18° γ: 90°
R-values:
R R work R free
0.188 0.188 0.198
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

2 review citations

Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.
Williamson et al. (2020)
1 more

2 mentions without citation

Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis.
Öz et al. (2021)
1 more