6dt1

X-ray diffraction
2.75Å resolution

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

Released:
Source organism: Escherichia virus T4
Entry authors: Shi K, Aihara H

Function and Biology Details

Reaction catalysed:
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase Chains: A, E
Molecule details ›
Chains: A, E
Length: 507 amino acids
Theoretical weight: 57.54 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P00970 (Residues: 1-487; Coverage: 100%)
Gene name: 30
Sequence domains: ATP dependent DNA ligase domain
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3') Chains: B, F
Molecule details ›
Chains: B, F
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: Escherichia virus T4
Expression system: Not provided
DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3') Chains: C, G
Molecule details ›
Chains: C, G
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: Escherichia virus T4
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 21 nucleotides
Theoretical weight: 6.39 KDa
Source organism: Escherichia virus T4
Expression system: Not provided

Ligands and Environments

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P1
Unit cell:
a: 63.526Å b: 67.429Å c: 114.635Å
α: 88.78° β: 80.94° γ: 62.97°
R-values:
R R work R free
0.172 0.17 0.219
Expression systems:
  • Escherichia coli
  • Not provided