431D

5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

B-DNA at atomic resolution reveals extended hydration patterns.

Vlieghe, D.Turkenburg, J.P.Van Meervelt, L.

(1999) Acta Crystallogr.,Sect.D 55: 1495-1502


  • PubMed Abstract: 
  • Despite the importance of hydration around DNA in the understanding of its conformation and interactions with other molecules in many biological processes, only limited atomic resolution information is available. Crystal-engineering techniques, which ...

    Despite the importance of hydration around DNA in the understanding of its conformation and interactions with other molecules in many biological processes, only limited atomic resolution information is available. Crystal-engineering techniques, which were originally developed to mimic DNA base triplets in a crystal lattice, also eliminate the rotational disorder of oligonucleotides around their helical axis and thereby enhance the resolution of the structure analysis. We have determined the low-temperature crystal structure of the synthetic DNA decamer d(GGCCAATTGG) at atomic resolution (1. 15 A) using 17700 reflections and have characterized the highly organized hydration patterns in both grooves. The narrow d(AATT) minor groove is occupied by an 'extended hydration spine' alternately bridging base pairs and phosphate O1P atoms of opposite strands, while a distinctive pattern of parallel water ribbons is observed in the major groove. This analysis provides structural insight into the correlation found between narrow minor-groove width and occurrence of the B(I) conformation and can be used to design new minor-groove binders. By their location between adjacent helices, two fully hydrated magnesium ions further stabilize the crystal packing. The structure also provides details of the hydration and conformation of G.GC triple helices.


    Related Citations: 
    • Parallel and Antiparallel (G-Gc)2 Triple Helix Fragments in a Crystal Structure
      Vlieghe, D.,Van Meervelt, L.,Dautant, A.,Gallois, B.,Precigoux, G.,Kennard, O.
      (1996) Science 273: 1702


    Organizational Affiliation

    Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 26.106α = 90.00
b = 36.455β = 90.00
c = 52.559γ = 90.00
Software Package:
Software NamePurpose
SHELXL-93refinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance