6LBW | pdb_00006lbw

Crystal structure of Ag-mediated base pairs in uncanonical DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb6LBW/pdb
• NAKB: 6LBW

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


• Deposited: 2019-11-15 Released: 2020-11-18 
• Deposition Author(s): Aoyama, H., Obika, S., Nakagawa, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids.

Nakagawa, O., Aoyama, H., Fujii, A., Kishimoto, Y., Obika, S.

(2021) Chemistry 27: 3842-3848

• PubMed: 33274789 
• DOI: https://doi.org/10.1002/chem.202004819
• Primary Citation Related Structures: 
  6LBW


• PubMed Abstract: 
  

  Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of Ag ^I ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of Ag ^I -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing Ag ^I -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of Ag ^I -mediated base pairs in the central region. The bent duplex structure induced by the addition of Ag ^I ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.
Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.13 kDa 
• Atom Count: 510 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*(CBR)P*GP*AP*(LCC)P*TP*CP*GP*CP*G)-3')	A, B	11	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	C [auth A], D [auth A]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.56	α = 90
b = 68.11	β = 90
c = 118.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Aoyama, H., Obika, S., Nakagawa, O.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2020-12-16
  Changes: Database references, Structure summary
• Version 1.2: 2020-12-23
  Changes: Database references
• Version 1.3: 2021-03-03
  Changes: Database references
• Version 1.4: 2024-03-27
  Changes: Data collection, Database references