3IJK | pdb_00003ijk

5-OMe modified DNA 8mer

• PDB DOI: https://doi.org/10.2210/pdb3IJK/pdb
• NAKB: 3IJK

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


• Deposited: 2009-08-04 Released: 2009-10-06 
• Deposition Author(s): Sheng, J., Zhang, W., Hassan, A.E.A., Gan, J., Huang, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate

Fang, Z., Dantsu, Y., Chen, C., Zhang, W., Huang, Z.

(2023) ChemistrySelect 8

• DOI: https://doi.org/10.1002/slct.202302253

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.52 kDa 
• Atom Count: 193 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'	A	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.190 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.21	α = 90
b = 43.21	β = 90
c = 23.692	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Sheng, J., Zhang, W., Hassan, A.E.A., Gan, J., Huang, Z.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-08-02
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description