3IFI | pdb_00003ifi

2'-SeMe-dG modified octamer DNA

• PDB DOI: https://doi.org/10.2210/pdb3IFI/pdb
• NAKB: 3IFI

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-07-24 Released: 2009-08-11 
• Deposition Author(s): Sheng, J., Gan, J., Salon, J., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.221 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Synthesis and crystal structure of 2'-se-modified guanosine containing DNA.

Salon, J., Sheng, J., Gan, J., Huang, Z.

(2010) J Org Chem 75: 637-641

• PubMed: 20047333 
• DOI: https://doi.org/10.1021/jo902190c
• Primary Citation Related Structures: 
  3IFI


• PubMed Abstract: 
  

  Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2'-SeMe-modified guanosine (G(Se)) phosphoramidite, and report the first incorporation of the 2'-Se-G moiety into DNA. The X-ray crystal structure of the 2'-Se-modified octamer DNA (5'-GTG(Se)TACAC-3') was determined at a resolution of 1.20 A. We also found that the 2'-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2'-Se-G modification can significantly facilitate the crystal growth with respect to the corresponding native DNA.

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Organizational Affiliation: 
• Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.52 kDa 
• Atom Count: 209 
• 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*(XUG)P*TP*AP*CP*AP*C)-3')	A	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.221 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.641	α = 90
b = 41.641	β = 90
c = 24.112	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Sheng, J., Gan, J., Salon, J., Huang, Z.

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description