2PL8

D(GTATACC) under hydrostatic pressure of 1.04 GPa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Adaptation of the base-paired double-helix molecular architecture to extreme pressure.

Girard, E.Prange, T.Dhaussy, A.C.Migianu-Griffoni, E.Lecouvey, M.Chervin, J.C.Mezouar, M.Kahn, R.Fourme, R.

(2007) Nucleic Acids Res. 35: 4800-4808

  • DOI: 10.1093/nar/gkm511
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The behaviour of the d(GGTATACC) oligonucleotide has been investigated by X-ray crystallography at 295 K in the range from ambient pressure to 2 GPa (approximately 20,000 atm). Four 3D-structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and ...

    The behaviour of the d(GGTATACC) oligonucleotide has been investigated by X-ray crystallography at 295 K in the range from ambient pressure to 2 GPa (approximately 20,000 atm). Four 3D-structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and 1.39 GPa) were refined at 1.60 or 1.65 A resolution. In addition to the diffraction pattern of the A-form, the broad meridional streaks previously explained by occluded B-DNA octamers within the channels of the crystalline A-form matrix were observed up to at least 2 GPa. This work highlights an important property of nucleic acids, their capability to withstand very high pressures, while keeping in such conditions a nearly invariant geometry of base pairs that store and carry genetic information. The double-helix base-paired architecture behaves as a molecular spring, which makes it especially adapted to very harsh conditions. These features may have contributed to the emergence of a RNA World at prebiotic stage.


    Related Citations: 
    • Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres.
      Kundrot, C.E.,Richards, F.M.
      (1987) J.Mol.Biol. 193: 157
    • Coexistence of A-and B-Form DNA in a Single Crystal Lattice
      Doucet, J.,Benoit, J.-P.,Cruse, W.B.T.,Prange, T.,Kennard, O.
      (1989) Nature 337: 190
    • High pressure macromolecular crystallography: The 140 MPa crystal structure at 2.3 A resolution of urate oxidase, A 135 KD tetrameric assembly
      Colloc'h, N.,Girard, E.,Dhaussy, A.C.,Kahn, R.,Ascone, I.,Mezouar, M.,Fourme, R.
      (2006) BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS 1764: 391
    • High-pressure protein crystallography (HPPX): Instrumentation, methodology and results on lysozyme crystals
      Fourme, R.,Kahn, R.,Mezouar, M.,Girard, E.,Horentrup, C.,Prange, T.,Ascone, I.
      (2001) J.Synchrotron Radia. 8: 1149


    Organizational Affiliation

    Synchrotron-SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France. eric.girard@synchrotron-soleil.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'A,B8N/A
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 43.423α = 90.00
b = 43.423β = 90.00
c = 40.450γ = 120.00
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SCALAdata scaling
XDSdata reduction
AUTOMARdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-01-17
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance