4YS5 | pdb_00004ys5

DNA sequence containing 2'-Se-dC modification

• PDB DOI: https://doi.org/10.2210/pdb4YS5/pdb
• NAKB: 4YS5

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


• Deposited: 2015-03-16 Released: 2016-02-24 
• Deposition Author(s): Kong, C., Zhang, W., Salon, J., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

DNA sequence containing 2'-Se-dC modification.

Kong, C., Zhang, W., Salon, J., Huang, Z.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.52 kDa 
• Atom Count: 177 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*GP*GP*(2SC)P*CP*AP*C)-3')	A	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.621	α = 90
b = 41.621	β = 90
c = 25.067	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Kong, C., Zhang, W., Salon, J., Huang, Z.

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations