› 6v6r

X-ray diffraction
2.7Å resolution

Crystal Structure of a Bromine Derivatized Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry.

Released:
DOI: 10.2210/pdb6v6r/pdb
PDB entry 6v6r coloured by chain, front view.
PDB entry 6v6r coloured by chain, side view.
PDB entry 6v6r coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H
Angew Chem Int Ed Engl 59 18619-18626 (2020)
PMID: 32533629

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120745 (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.36 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3') Chain: A
Molecule details ›
Chain: A
Length: 7 nucleotides
Theoretical weight: 2.15 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*CP*AP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.52 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CAC 2 x CAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: R3
Unit cell:
a: 115.806Å b: 115.806Å c: 44.748Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.244 0.242 0.279
Expression system: Not provided

Quick links

Citations

4 review citations

The interactions between DNA nanostructures and cells: A critical overview from a cell biology perspective.
Frtús et al. (2022)
3 more