1RRU

The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The Influence of a Chiral Amino Acid on the Helical Handedness of PNA in Solution and in Crystals

Rasmussen, H.Liljefors, T.Petersson, B.Nielsen, P.E.Kastrup, J.S.

(2004) J Biomol Struct Dyn 21: 495-502

  • DOI: https://doi.org/10.1080/07391102.2004.10506943
  • Primary Citation of Related Structures:  
    1RRU

  • PubMed Abstract: 

    The X-ray structure of a self-complementary PNA hexamer (H-CGTACG-L-Lys-NH(2)) has been determined to 2.35 A resolution. The introduction of an L-lysine moiety has previously been shown to induce a preferred left-handedness of the PNA double helices in aqueous solution. However, in the crystal structure an equal amount of interchanging right- and left-handed helices is observed. The lysine moieties are pointing into large solvent channels and no significant interactions between this moiety and the remaining PNA molecule are observed. In contrast, molecular mechanics calculations show a preference for the left-handed helix of this hexameric PNA in aqueous solution as expected. The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution.


  • Organizational Affiliation

    Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100, Copenhagen, Denmark.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)
A, B
8N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.75α = 90
b = 44.07β = 91.51
c = 31.22γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-08-28
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations