› 3ndh

X-ray diffraction
1.3Å resolution

Restriction endonuclease in complex with substrate DNA

Released:
DOI: 10.2210/pdb3ndh/pdb
PDB entry 3ndh coloured by chain, front view.
PDB entry 3ndh coloured by chain, side view.
PDB entry 3ndh coloured by chain, top view.
Source organism: Thermoplasma acidophilum
Primary publication:
DNA intercalation without flipping in the specific ThaI-DNA complex.
Firczuk M, Wojciechowski M, Czapinska H, Bochtler M
Nucleic Acids Res 39 744-54 (2011)
PMID: 20861000

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116612 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II restriction endonuclease subunit R Chains: A, B
Molecule details ›
Chains: A, B
Length: 225 amino acids
Theoretical weight: 26.42 KDa
Source organism: Thermoplasma acidophilum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HJY3 (Residues: 2-216; Coverage: 100%)
Gene name: Ta0828
Sequence domains: Restriction endonuclease ThaI
Structure domains: ECO RV Endonuclease; Chain A
DNA (5'-D(*G*GP*TP*AP*CP*GP*CP*GP*AP*TP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.41 KDa
Source organism: Thermoplasma acidophilum
Expression system: Not provided
DNA (5'-D(*C*CP*AP*TP*CP*GP*CP*GP*TP*AP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: Thermoplasma acidophilum
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand NA 2 x NA
Ligand CL 2 x CL
Ligand PGE 3 x PGE
Ligand ACT 4 x ACT
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P21
Unit cell:
a: 39.31Å b: 72.91Å c: 88.76Å
α: 90° β: 101.99° γ: 90°
R-values:
R R work R free
0.172 0.172 0.183
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 citation in other articles

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
Steczkiewicz et al. (2012)
7 more

3 mentions without citation

A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.
Chang et al. (2015)
2 more