6IYQ

Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides

• PDB DOI: https://doi.org/10.2210/pdb6IYQ/pdb
• NAKB: 6IYQ

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


• Deposited: 2018-12-17 Released: 2019-10-30 
• Deposition Author(s): Kondo, J., Ono, A., Atsugi, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.282 
• R-Value Work: 0.247 
• R-Value Observed: 0.251 

Literature

Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides: reversible formation and cleavage catalyzed by Cu(II) ion and glutathione

Ono, A., Atsugi, T., Goto, M., Saneyoshi, H., Tomori, T., Seio, K., Dairaku, T., Kondo, J.

(2019) RSC Adv 

Biological Assembly 1  

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 7.6 kDa 
• Atom Count: 494 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*(S6G)P*(S6G)P*(BRU)P*CP*GP*CP*G)-3')	A, B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.282 
• R-Value Work: 0.247 
• R-Value Observed: 0.251 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.254	α = 90
b = 46.522	β = 90
c = 76.084	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Kondo, J., Ono, A., Atsugi, T.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references