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› 6xdv

X-ray diffraction
3Å resolution

Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J3 immobile Holliday junction

Released:
DOI: 10.2210/pdb6xdv/pdb
Model geometry
Fit model/data
PDB entry 6xdv coloured by chain, front view.
PDB entry 6xdv coloured by chain, side view.
PDB entry 6xdv coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.
Simmons CR, MacCulloch T, Krepl M, Matthies M, Buchberger A, Crawford I, Šponer J, Šulc P, Stephanopoulos N, Yan H
OpenAccess logo Nat Commun 13 3112 (2022)
PMID: 35662248

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-120930 (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*GP*TP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 11 nucleotides
Theoretical weight: 3.42 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 2.95 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*AP*AP*GP*T)-3') Chain: C
DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*CP*GP*TP*CP*TP*GP*C)-3') Chain: D

Ligands and Environments

1 bound ligand:
Ligand CAC 3 x CAC
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P32
Unit cell:
a: 68.932Å b: 68.932Å c: 60.748Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.23 0.227 0.252
Expression system: Not provided

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Citations

4 review citations

The development of nucleic acids force fields: From an unchallenged past to a competitive future.
Liebl et al. (2023)
3 more