1I1P

REFINEMENT INCLUDING EXPERIMENTAL MAD PHASES ALLOWS AN EXHAUSTIVE STUDY OF ORDERED SOLVENT MOLECULES FOR A PLATINATED DECANUCLEOTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6A resolution against experimental MAD phases.

Coste, F.Shepard, W.Zelwer, C.

(2002) Acta Crystallogr.,Sect.D 58: 431-440


  • PubMed Abstract: 
  • Accurate experimental phases derived from a MAD experiment may be useful to enable the identification of solvent molecules during the course of an atomic parameter refinement. The structure of a double-stranded DNA decanucleotide bearing a cisplatin ...

    Accurate experimental phases derived from a MAD experiment may be useful to enable the identification of solvent molecules during the course of an atomic parameter refinement. The structure of a double-stranded DNA decanucleotide bearing a cisplatin interstrand cross-link at 1.6A resolution, whose phases were first determined experimentally using the L(III) edge of the Pt atom, was refined by various methods. The previously published structure resulted from a least-squares refinement using the structure-factor magnitudes and stereochemical restraints (program SHELX). In this paper, these previous results are compared with a model obtained by the likelihood-maximization method (program REFMAC) which allows the combination of the observed magnitudes with experimental MAD phases. This solution corresponded to a lower R(free) (18.8 compared with 20.3%), a lower R factor and accounted for 135 water molecules and one spermine molecule collected by the program wARP during refinement. The previously published SHELX solution exhibited no spermine molecule and accounted for 92 water molecules, only 74 of which are also present in the model obtained with the MAD phases. In order to verify that these improvements were actually related to the use of the MAD phases, the same type of procedure without the MAD phases was applied starting from the initial model. The resulting solution had a higher R(free) (20.3%), which could be related to the loss of 22 water molecules and the addition of 20 new ones. MAD phases therefore seem especially helpful in preventing the model bias which may affect the solvent molecules. All models have in common a hydration cage of nine water molecules which surround the platinum residue. In addition to the spermine molecule, the model obtained with the MAD phases allows description of the water-molecule organization, with reproducible motifs related to the base pairs and to the phosphodiester backbone.


    Related Citations: 
    • Crystal Structure of a Double-Stranded DNA Containing A Cisplatin Interstrand Cross-Link At 1.63 Angstrom Resolution: Hydration At The Platinated Site
      Coste, F.,Malinge, J.M.,Serre, L.,Shepard, W.,Roth, M.,Leng, M.,Zelwer, C.
      (1999) Nucleic Acids Res. 27: 1837


    Organizational Affiliation

    Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, University of Orléans and Institut National de la Santé et de la Recherche Médicale, Rue Charles Sadron, 45071 Orléans CEDEX 2, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3'A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3'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
CPT
Query on CPT

Download SDF File 
Download CCD File 
A
Cisplatin
diammine(dichloro)platinum
Cl2 H6 N2 Pt
LXZZYRPGZAFOLE-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 42.890α = 90.00
b = 29.980β = 95.98
c = 46.570γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
MOSFLMdata reduction
CCP4data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance