› 7sdh

X-ray diffraction
4.05Å resolution

[S:Ag+:S] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice

Released:
DOI: 10.2210/pdb7sdh/pdb
PDB entry 7sdh coloured by chain, front view.
PDB entry 7sdh coloured by chain, side view.
PDB entry 7sdh coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.
Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R
Adv Mater e2201938 (2023)
PMID: 36939292

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121970 (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(IMC)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3') Chain: A
Molecule details ›
Chain: A
Length: 21 nucleotides
Theoretical weight: 6.46 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*CP*AP*(IMC)P*AP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 7 nucleotides
Theoretical weight: 2.07 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.13 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 7 nucleotides
Theoretical weight: 2.13 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand AG 1 x AG
1 modified residue:
Ligand IMC 2 x IMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: R3
Unit cell:
a: 105.857Å b: 105.857Å c: 93.859Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.184 0.236
Expression system: Not provided

Quick links

Citations

1 mention without citation

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications.
Burguera et al. (2023)