7URK | pdb_00007urk

Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification

• PDB DOI: https://doi.org/10.2210/pdb7URK/pdb
• NAKB: 7URK

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2022-04-22 Released: 2023-04-26 
• Deposition Author(s): Sha, R., Vecchioni, S.
• Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States), Human Frontier Science Program (HFSP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification

Sha, R., Vecchioni, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 13.23 kDa 
• Atom Count: 870 
• Modeled Residue Count: 43 
• Deposited Residue Count: 43 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')	A	13	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')	B	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')	C	14	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	D	9	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.785	α = 90
b = 113.785	β = 90
c = 95.709	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Sha, R., Vecchioni, S.

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Funding Organization	Location	Grant Number
Office of Naval Research (ONR)	United States	N000141912596
Department of Energy (DOE, United States)	United States	DE-SC0007991
National Science Foundation (NSF, United States)	United States	2106790
Human Frontier Science Program (HFSP)	France	RPG0010/2017
National Science Foundation (NSF, United States)	United States	DMR-1420073

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description