› 7jkd

X-ray diffraction
3.06Å resolution

Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J1 immobile Holliday junction

Released:
DOI: 10.2210/pdb7jkd/pdb
PDB entry 7jkd coloured by chain, front view.
PDB entry 7jkd coloured by chain, side view.
PDB entry 7jkd 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-121346 (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*TP*GP*AP*CP*GP*GP*AP*GP*AP*CP*TP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 21 nucleotides
Theoretical weight: 6.47 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.77 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 8 nucleotides
Theoretical weight: 2.42 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*GP*TP*CP*GP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P32
Unit cell:
a: 67.97Å b: 67.97Å c: 55.829Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.239 0.236 0.27
Expression system: Not provided

Quick links

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