› 6ukf

X-ray diffraction
1Å resolution

HhaI endonuclease in Complex with DNA at 1 Angstrom Resolution

Released:
DOI: 10.2210/pdb6ukf/pdb
PDB entry 6ukf coloured by chain, front view.
PDB entry 6ukf coloured by chain, side view.
PDB entry 6ukf coloured by chain, top view.
Source organism: Haemophilus parahaemolyticus
Primary publication:
Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å.
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X
Nucleic Acids Res 48 1466-1478 (2020)
PMID: 31879785

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120707 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
HhaI Restriction Endonuclease Chain: X
Molecule details ›
Chain: X
Length: 258 amino acids
Theoretical weight: 29.98 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Escherichia coli
UniProt:
  • Canonical: I3DBY6 (Residues: 1-258; Coverage: 100%)
Gene name: HMPREF1050_0931
DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Not provided
DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.22 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand EDO 16 x EDO
Ligand ACT 1 x ACT
Ligand PO4 1 x PO4
Ligand CA 1 x CA
1 modified residue:
Ligand 5IU 2 x 5IU

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 61.018Å b: 37.317Å c: 69.027Å
α: 90° β: 109.768° γ: 90°
R-values:
R R work R free
0.155 0.155 0.166
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 citation in other articles

Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P.
Zhu et al. (2022)
1 more

1 mention without citation

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å.
Horton et al. (2020)