PDBe 2q2t

X-ray diffraction
2.3Å resolution

Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
ATP-dependent DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 319 amino acids
Theoretical weight: 36.83 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O41026 (Residues: 1-298; Coverage: 100%)
Gene name: A544R
Sequence domains:
Structure domains:
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: Paramecium bursaria Chlorella virus 1
Expression system: Not provided
5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.34 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided
5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 66.301Å b: 81.29Å c: 96.418Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.261
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided