› 7obn

X-ray diffraction
2.45Å resolution

Structural investigations of a new L3 DNA ligase: structure-function analysis

Released:
DOI: 10.2210/pdb7obn/pdb
PDB entry 7obn coloured by chain, front view.
PDB entry 7obn coloured by chain, side view.
PDB entry 7obn coloured by chain, top view.
Source organisms:
Primary publication:
Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase.
Pan J, Lian K, Sarre A, Leiros HS, Williamson A
OpenAccess logo Sci Rep 11 18693 (2021)
PMID: 34548548

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-241162 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 321 amino acids
Theoretical weight: 35.66 KDa
Source organism: Burkholderia pseudomallei
Expression system: Escherichia coli
DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand AMP 1 x AMP
Ligand SO4 1 x SO4
1 modified residue:
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 125.473Å b: 45.552Å c: 111.459Å
α: 90° β: 103.939° γ: 90°
R-values:
R R work R free
0.259 0.257 0.283
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Expanding the viewpoint: Leveraging sequence information in enzymology.
Knox et al. (2023)

1 mention without citation

Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase.
Pan et al. (2021)