3GJL

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

• PDB DOI: https://doi.org/10.2210/pdb3GJL/pdb
• NAKB: 3GJL

• 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., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.264 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

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.M., William, D.M.

To be published.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 3.68 kDa 
• Atom Count: 289 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3'	B	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.264 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.477	α = 90
b = 26.477	β = 90
c = 98.958	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	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., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.

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