› 3p4h

X-ray diffraction
1.1Å resolution

Structures of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily

Released:
DOI: 10.2210/pdb3p4h/pdb
Model geometry
Fit model/data
PDB entry 3p4h coloured by chain, front view.
PDB entry 3p4h coloured by chain, side view.
PDB entry 3p4h coloured by chain, top view.
Source organism: Candidatus Korarchaeum cryptofilum OPF8
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
OpenAccess logo 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-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 OPF8
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 MN 1 x MN
Ligand PO4 1 x PO4
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 27.769Å b: 58.458Å c: 33.18Å
α: 90° β: 102.25° γ: 90°
R-values:
R R work R free
0.135 0.132 0.165
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 citation in other articles

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

5 mentions without citation

Protein evolution along phylogenetic histories under structurally constrained substitution models.
Arenas et al. (2013)
4 more