› 3ta5

X-ray diffraction
1.52Å resolution

Cobalt bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family

Released:
DOI: 10.2210/pdb3ta5/pdb
PDB entry 3ta5 coloured by chain, front view.
PDB entry 3ta5 coloured by chain, side view.
PDB entry 3ta5 coloured by chain, top view.
Source organism: Candidatus Korarchaeum cryptofilum
Primary publication:
Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Das U, Smith P, Shuman S
Nucleic Acids Res 40 828-36 (2012)
PMID: 21965539

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109327 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase D 3'-phosphoesterase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 118 amino acids
Theoretical weight: 13.85 KDa
Source organism: Candidatus Korarchaeum cryptofilum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1L4V6 (Residues: 1-117; Coverage: 100%)
Gene name: Kcr_0736
Sequence domains: DNA polymerase Ligase (LigD)

Ligands and Environments

3 bound ligands:
Ligand CO 1 x CO
Ligand PO4 1 x PO4
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 27.74Å b: 58.4Å c: 33.05Å
α: 90° β: 102.55° γ: 90°
R-values:
R R work R free
0.16 0.156 0.189
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

RNA-Independent DNA Cleavage Activities of Cas9 and Cas12a.
Sundaresan et al. (2017)
2 more

1 mention without citation

Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Das et al. (2012)