9YBK | pdb_00009ybk

[2ULA] Double crossover-like L-DNA motif containing a mobile junction

• PDB DOI: https://doi.org/10.2210/pdb9YBK/pdb
• NAKB: 9YBK

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


• Deposited: 2025-09-17 Released: 2025-10-22 
• Deposition Author(s): Horvath, A., Singh, V.R., Vecchioni, S., Ohayon, Y.P., Sha, R.
• Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.258 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Mobile Junction in Double Crossover-Like Tiles

Singh, V.R., Horvath, A., Vecchioni, S., Ohayon, Y.P., Sha, R.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 9.82 kDa 
• Atom Count: 651 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(0DT)P*(0DG)P*(0DA)P*(0DC)P*(0DG)P*(0DG)P*(0DC)P*(0DT)P*(0DG)P*(0DG)P*(0DA)P*(0DC)P*(0DT)P*(0DC)P*(0DG)P*(0DT))-3')	A	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(0DC)P*(0DA)P*(0DA)P*(0DG)P*(0DC)P*(0DC)P*(0DG)P*(0DT)P*(0DG)P*(0DA)P*(0DG)P*(0DT)P*(0DC)P*(0DC)P*(0DA)P*(0DC))-3')	B	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.985	α = 90
b = 35.985	β = 90
c = 102.023	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Horvath, A., Singh, V.R., Vecchioni, S., Ohayon, Y.P., Sha, R.

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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	CCF-2106790
National Science Foundation (NSF, United States)	United States	GCR-2317843

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release