› 4par

X-ray diffraction
2.89Å resolution

The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with Product-like DNA

Released:
DOI: 10.2210/pdb4par/pdb
PDB entry 4par coloured by chain, front view.
PDB entry 4par coloured by chain, side view.
PDB entry 4par coloured by chain, top view.
Source organisms:
Primary publication:
Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.
Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X
Nucleic Acids Res 42 7947-59 (2014)
PMID: 24895434

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109253 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Uncharacterized protein AbaSI Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 321 amino acids
Theoretical weight: 37.67 KDa
Source organism: Acinetobacter baumannii SDF
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B0VN39 (Residues: 1-321; Coverage: 100%)
Gene name: ABSDF3356
Sequence domains:
DNA 18-MER Chains: E, F
Molecule details ›
Chains: E, F
Length: 18 nucleotides
Theoretical weight: 5.53 KDa
Source organism: Tequatrovirus
Expression system: Not provided
DNA 14-MER Chains: G, H
Molecule details ›
Chains: G, H
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
Source organism: Tequatrovirus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand EDO 1 x EDO
1 modified residue:
Ligand 5HC 2 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 54.826Å b: 144.704Å c: 105.033Å
α: 90° β: 94.57° γ: 90°
R-values:
R R work R free
0.193 0.19 0.249
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.
Hong et al. (2016)
19 other articles

3 mentions without citation

Desminopathies: pathology and mechanisms.
Clemen et al. (2013)
2 more