› 3ubi

X-ray diffraction
6.8Å resolution

The Absence of Tertiary Interactions in a Self-Assembled DNA Crystal Structure

Released:
DOI: 10.2210/pdb3ubi/pdb
PDB entry 3ubi coloured by chain, front view.
PDB entry 3ubi coloured by chain, side view.
PDB entry 3ubi coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
The absence of tertiary interactions in a self-assembled DNA crystal structure.
Nguyen N, Birktoft JJ, Sha R, Wang T, Zheng J, Constantinou PE, Ginell SL, Chen Y, Mao C, Seeman NC
J Mol Recognit 25 234-7 (2012)
PMID: 22434713

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116977 (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
Source organism: Synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.23 KDa
Source organism: Synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: R3
Unit cell:
a: 169.98Å b: 169.98Å c: 88.638Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.14 0.138 0.152
Expression system: Not provided

Quick links

Citations

3 review citations

DNA-based construction at the nanoscale: emerging trends and applications.
Xavier et al. (2018)
2 more

4 mentions without citation

The wending rhombus: Self-assembling 3D DNA crystals.
Lu et al. (2022)
3 more