› 3p43

X-ray diffraction
2.1Å resolution

Structure and Activities of Archaeal Members of the LigD 3' Phosphoesterase DNA Repair Enzyme Superfamily

Released:
DOI: 10.2210/pdb3p43/pdb
PDB entry 3p43 coloured by chain, front view.
PDB entry 3p43 coloured by chain, side view.
PDB entry 3p43 coloured by chain, top view.
Source organism: Methanosarcina barkeri str. Fusaro
Primary publication:
Structures and activities of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily.
Smith P, Nair PA, Das U, Zhu H, Shuman S
Nucleic Acids Res 39 3310-20 (2011)
PMID: 21208981

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-175173 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase D 3'-phosphoesterase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 17.58 KDa
Source organism: Methanosarcina barkeri str. Fusaro
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q46AP6 (Residues: 1-151; Coverage: 100%)
Gene name: Mbar_A2115
Sequence domains: DNA polymerase Ligase (LigD)

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand CL 1 x CL
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 30.368Å b: 60.166Å c: 76.471Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.203 0.257
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 citation in other articles

Ribonucleolytic resection is required for repair of strand displaced nonhomologous end-joining intermediates.
Bartlett et al. (2013)
7 more

2 mentions without citation

An integrated linkage, chromosome, and genome map for the yellow fever mosquito Aedes aegypti.
Timoshevskiy et al. (2013)
1 more