3NAO

A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit Cell

• PDB DOI: https://doi.org/10.2210/pdb3NAO/pdb
• NAKB: 3NAO

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-06-02 Released: 2011-11-30 
• Deposition Author(s): Wang, T., Sha, R., Birktoft, J.J., Zheng, J., Mao, M., Seeman, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.03 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

A DNA crystal designed to contain two molecules per asymmetric unit.

Wang, T., Sha, R., Birktoft, J., Zheng, J., Mao, C., Seeman, N.C.

(2010) J Am Chem Soc 132: 15471-15473

• PubMed: 20958065 
• DOI: https://doi.org/10.1021/ja104833t
• Primary Citation of Related Structures:  
  3NAO


• PubMed Abstract: 
  

  We describe the self-assembly of a DNA crystal that contains two tensegrity triangle molecules per asymmetric unit. We have used X-ray crystallography to determine its crystal structure. In addition, we have demonstrated control over the colors of the crystals by attaching either Cy3 dye (pink) or Cy5 dye (blue-green) to the components of the crystal, yielding crystals of corresponding colors. Attaching the pair of dyes to the pair of molecules yields a purple crystal.

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Organizational Affiliation: 

Department of Chemistry, New York University, New York, New York 10003, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.6 kDa 
• Atom Count: 1,710 
• Modelled Residue Count: 84 
• Deposited Residue Count: 84 
• Unique nucleic acid chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	A	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')	B	7	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')	C	6	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*T)-3')	D	8	N/A

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*CP*TP*AP*CP*CP*TP*GP*CP*GP*TP*GP*GP*AP*CP*AP*GP*AP*C)-3')	E	21	N/A

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*CP*GP*CP*A)-3')	F	7	N/A

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*TP*AP*GP*G)-3')	G	6	N/A

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*GP*TP*CP*TP*GP*T)-3')	H	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.03 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.345	α = 90
b = 105.345	β = 90
c = 183.938	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-30 
Deposition Author(s): Wang, T., Sha, R., Birktoft, J.J., Zheng, J., Mao, M., Seeman, N.C.

Revision History  

• Version 1.0: 2011-11-30
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Experimental preparation
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations