› 5keo

X-ray diffraction
3.15Å resolution

Structure Determination of a Self-Assembling DNA Crystal

Released:
DOI: 10.2210/pdb5keo/pdb
PDB 5keo coloured by chain and viewed from the front.
PDB 5keo coloured by chain and viewed from the side.
PDB 5keo coloured by chain and viewed from the top.
Source organism: Endothia gyrosa
Primary publication:
Construction and Structure Determination of a Three-Dimensional DNA Crystal.
Simmons CR, Zhang F, Birktoft JJ, Qi X, Han D, Liu Y, Sha R, Abdallah HO, Hernandez C, Ohayon YP, Seeman NC, Yan H
J. Am. Chem. Soc. (2016)
PMID: 27447429

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3') Chain: A
Molecule details ›
Chain: A
Length: 21 nucleotides
Theoretical weight: 6.43 KDa
Source organism: Endothia gyrosa
Expression system: Not provided
DNA (5'-D(P*CP*GP*TP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.48 KDa
Source organism: Endothia gyrosa
Expression system: Not provided
DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Endothia gyrosa
Expression system: Not provided
DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 7 nucleotides
Theoretical weight: 2.13 KDa
Source organism: Endothia gyrosa
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: NSLS BEAMLINE X25
Spacegroup: P3221
Unit cell:
a: 67.946Å b: 67.946Å c: 58.839Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.232 0.275
Expression system: Not provided

Quick links

Citations

5 review citations

Amphiphilic DNA nanostructures for bottom-up synthetic biology.
Rubio-Sánchez et al. (2021)
4 more