1DPL

A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 
    0.121 (Depositor), 0.140 (DCC) 
  • R-Value Work: 
    0.115 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.117 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SPMClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution.

Egli, M.Tereshko, V.Teplova, M.Minasov, G.Joachimiak, A.Sanishvili, R.Weeks, C.M.Miller, R.Maier, M.A.An, H.Dan Cook, P.Manoharan, M.

(1998) Biopolymers 48: 234-252

  • DOI: https://doi.org/10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H
  • Primary Citation of Related Structures:  
    1DPL, 1DPN

  • PubMed Abstract: 

    We have determined single crystal structures of an A-DNA decamer and a B-DNA dodecamer at 0.83 and 0.95 A, respectively. The resolution of the former is the highest reported thus far for any right-handed nucleic acid duplex and the quality of the diffraction data allowed determination of the structure with direct methods. The structures reveal unprecedented details of DNA fine structure and hydration; in particular, we have reexamined the overall hydration of A- and B-form DNA, the distribution of water around phosphate groups, and features of the water structure that may underlie the B to A transition.


  • Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry and The Drug Discovery Program, Northwestern University Medical School, Chicago, IL 60611, USA. m-egli@nwu.edu


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'
A, B
10N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free:  0.121 (Depositor), 0.140 (DCC) 
  • R-Value Work:  0.115 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.117 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.627α = 90
b = 42.717β = 90
c = 46.906γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SPMClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2022-06-22
    Changes: Data collection, Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2024-02-07
    Changes: Data collection