3FX8 | pdb_00003fx8

Distinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate')

• PDB DOI: https://doi.org/10.2210/pdb3FX8/pdb
• NAKB: 3FX8

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-01-20 Released: 2010-03-16 
• Deposition Author(s): Boer, D.R., Uson, I., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.212 (Depositor) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders.

Boer, D.R., Kerckhoffs, J.M., Parajo, Y., Pascu, M., Uson, I., Lincoln, P., Hannon, M.J., Coll, M.

(2010) Angew Chem Int Ed Engl 49: 2336-2339

• PubMed: 20191645 
• DOI: https://doi.org/10.1002/anie.200906742
• Primary Citation of Related Structures:  
  3FX8, 3I1D

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Organizational Affiliation: 

Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 2.82 kDa 
• Atom Count: 182 
• Modelled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
(5'-D(*CP*GP*TP*AP*CP*G)-3'	A [auth C]	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5PM	F [auth C], G [auth C]	4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline} C24 H18 N4 S KHOHHSYBCGDFBZ-XUIWWLCJSA-N
FE2	B [auth C], C, D [auth C], E [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.212 (Depositor) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.249	α = 90
b = 49.249	β = 90
c = 49.249	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
SHELXDE	phasing
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Boer, D.R., Uson, I., Coll, M.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations