4LTG

Dehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 74% relative humidity (2/7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.089 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Controlled Dehydration of a Ruthenium Complex-DNA Crystal Induces Reversible DNA Kinking.

Hall, J.P.Sanchez-Weatherby, J.Alberti, C.Quimper, C.H.O'Sullivan, K.Brazier, J.A.Winter, G.Sorensen, T.Kelly, J.M.Cardin, D.J.Cardin, C.J.

(2014) J.Am.Chem.Soc. 136: 17505-17512

  • DOI: 10.1021/ja508745x
  • Primary Citation of Related Structures:  4LTF, 4LTH, 4LTI, 4LTJ, 4LTK, 4LTL

  • PubMed Abstract: 
  • Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crysta ...

    Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.


    Organizational Affiliation

    Chemistry Department, University of Reading , Whiteknights, Reading, Berkshire RG6 6AD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNAA10N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BA
Query on BA

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Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
RKL
Query on RKL

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Download CCD File 
A
Ru(tap)2(dppz) complex
C38 H22 N12 Ru
PIKVAZQLFXBUSD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.089 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 44.300α = 90.00
b = 44.300β = 90.00
c = 27.550γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
GDAdata collection
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2015-01-07
    Type: Database references
  • Version 1.3: 2017-03-08
    Type: Other