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 
  • R-Value Work: 0.115 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H
  • Primary Citation of Related Structures:  

  • 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 dif ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'A,B10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
B
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
T23
Query on T23
A, B
RNA LINKINGC12 H19 N2 O8 PT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.115 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.627α = 90.00
b = 42.717β = 90.00
c = 46.906γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance