2GPX

2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC

  • Classification: DNA

  • Deposited: 2006-04-18 Released: 2006-05-23 
  • Deposition Author(s): Jiang, J., Huang, Z.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selenium derivatization of nucleic acids for crystallography.

Jiang, J.Sheng, J.Carrasco, N.Huang, Z.

(2007) Nucleic Acids Res. 35: 477-485

  • DOI: 10.1093/nar/gkl1070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 A resolution) with the 2'-Se modification in the min ...

    The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 A resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 A). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 A resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native and Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.


    Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'A8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download SDF File 
Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
A
DNA LINKINGC9 H12 Br N2 O8 PDU
UMS
Query on UMS
A
DNA LINKINGC10 H15 N2 O8 P SeDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.252α = 90.00
b = 42.252β = 90.00
c = 24.133γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CBASSdata collection
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-04-18 
  • Released Date: 2006-05-23 
  • Deposition Author(s): Jiang, J., Huang, Z.

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance