2PLB | pdb_00002plb

D(GTATACC) under hydrostatic pressure of 1.39 GPa

• PDB DOI: https://doi.org/10.2210/pdb2PLB/pdb
• NAKB: 2PLB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2007-04-19 Released: 2007-07-24 
• Deposition Author(s): Prange, T., Girard, E., Kahn, R., Fourme, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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

• PubMed: 17617642 
• DOI: https://doi.org/10.1093/nar/gkm511
• Primary Citation Related Structures: 
  2PKV, 2PL4, 2PL8, 2PLB


• 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 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.

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Organizational Affiliation: 
• Synchrotron-SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.06 kDa 
• Atom Count: 435 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'	A, B	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	C [auth B]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.83	α = 90
b = 42.83	β = 90
c = 40.3	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
AUTOMAR	data collection
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Prange, T., Girard, E., Kahn, R., Fourme, R.

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2008-01-17
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description