1G8V

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?

Tsunoda, M.Karino, N.Ueno, Y.Matsuda, A.Takenaka, A.

(2001) Acta Crystallogr.,Sect.D 57: 345-348

  • Primary Citation of Related Structures:  1G75, 1G8N, 1G8U

  • PubMed Abstract: 
  • To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2'-deoxy-5-formyluridine at X, were obtained under several conditions with and without ...

    To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2'-deoxy-5-formyluridine at X, were obtained under several conditions with and without divalent cations. The crystal structures are all isomorphous. The octahedrally hydrated magnesium cations found in the major groove cement the two neighbouring duplexes along the b axis. In the Mg(2+)-free crystals, a five-membered ring of water molecules occupies the same position as the magnesium site and connects the two duplexes similarly to the hydrated Mg(2+) ion. It has been concluded that water molecules can take the place of the hydrated magnesium cation in crystallization, but the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution. In all four crystals, the 5-formyluracil residues form the canonical Watson-Crick pair with adenine residues.


    Organizational Affiliation

    Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*AP*AP*TP*(UFR)P*CP*GP*CP*G)-3'A,B12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UFR
Query on UFR
A, B
DNA LINKINGC10 H13 N2 O9 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.300α = 90.00
b = 41.700β = 90.00
c = 66.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance