› 5keo

X-ray diffraction
3.15Å resolution

Structure Determination of a Self-Assembling DNA Crystal

Released:
DOI: 10.2210/pdb5keo/pdb
PDB entry 5keo coloured by chain, front view.
PDB entry 5keo coloured by chain, side view.
PDB entry 5keo coloured by chain, top view.
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 138 10047-54 (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)
Assembly name:
PDBe Complex ID:
PDB-CPX-118911 (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

11 review citations

Building machines with DNA molecules.
Ramezani et al. (2020)
10 more