4LTH

Dehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 97% relative humidity (3/7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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Ligand Structure Quality Assessment 


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, 4LTG, 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 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 ...

    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

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNAA10N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RKL
Query on RKL

Download Ideal Coordinates CCD File 
B [auth A]Ru(tap)2(dppz) complex
C38 H22 N12 Ru
PIKVAZQLFXBUSD-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

Download Ideal Coordinates CCD File 
C [auth A]BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.98α = 90
b = 42.98β = 90
c = 39.42γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2015-01-07
    Changes: Database references
  • Version 1.3: 2018-04-18
    Changes: Data collection