› 3sz4

X-ray diffraction
2.59Å resolution

Crystal Structure of LHK-Exo in complex with dAMP

Released:
DOI: 10.2210/pdb3sz4/pdb
PDB entry 3sz4 coloured by chain, front view.
PDB entry 3sz4 coloured by chain, side view.
PDB entry 3sz4 coloured by chain, top view.
Source organism: Laribacter hongkongensis HLHK9
Primary publication:
Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis.
Yang W, Chen WY, Wang H, Ho JW, Huang JD, Woo PC, Lau SK, Yuen KY, Zhang Q, Zhou W, Bartlam M, Watt RM, Rao Z
OpenAccess logo Nucleic Acids Res 39 9803-19 (2011)
PMID: 21893587

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111083 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YqaJ viral recombinase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 216 amino acids
Theoretical weight: 24.48 KDa
Source organism: Laribacter hongkongensis HLHK9
Expression system: Escherichia coli
UniProt:
  • Canonical: C1D7P6 (Residues: 1-203; Coverage: 100%)
Gene name: LHK_01497
Sequence domains: YqaJ-like viral recombinase domain
Structure domains: Lambda Exonuclease; Chain A

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand D5M 1 x D5M
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P63
Unit cell:
a: 108.327Å b: 108.327Å c: 47.824Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.208 0.262
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Structure and mechanism of the Red recombination system of bacteriophage λ.
Caldwell et al. (2019)
1 more

2 mentions without citation

Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus.
Lemak et al. (2013)
1 more