3GJH

Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

• PDB DOI: https://doi.org/10.2210/pdb3GJH/pdb
• NAKB: 3GJH

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-03-09 Released: 2010-03-31 
• Deposition Author(s): Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.306 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one

Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L.

To be published.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 7.68 kDa 
• Atom Count: 529 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAP	C [auth B]	6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE C16 H15 N5 FWBHETKCLVMNFS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.306 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.207	α = 90
b = 41.379	β = 90
c = 64.866	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description