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 1.2 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: 10.1080/07391102.2004.10506943

  • 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 ...

    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.


    Related Citations: 
    • Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution
      Rasmussen, H.,Kastrup, J.S.,Nielsen, J.N.,Nielsen, J.M.,Nielsen, P.E.
      (1997) Nat.Struct.Mol.Biol. 4: 98
    • Peptide nucleic acids (PNA) derived from N-(N-methylaminoethyl) glycine. Synthesis, hybridization and structural properties
      Haiima, G.,Rasmussen, H.,Schmidt, G.,Jensen, D.K.,Kastrup, J.S.,Stafshede, P.W.,Norden, B.,Buckhardt, O.,Nielsen, P.E.
      (1999) New J.Chem. 23: 833
    • 1,8-Naphthyridin-2(1H)-ones. Novel bi- and tricyclic analogues of Thymine in Peptide nucleic acids (PNA)
      Eldrup, A.B.,Nielsen, B.B.,Haiima, G.,Rasmussen, H.,Kastrup, J.S.,Christensen, C.,Nielsen, P.E.
      (2001) Eur.J.Org.Chem. --: 1781


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)A,B8N/A
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B
NON-POLYMERH2 N

--

CPN
Query on CPN
A, B
PEPTIDE-LIKEC10 H16 N5 O4

--

TPN
Query on TPN
A, B
PEPTIDE-LIKEC11 H17 N4 O5

--

GPN
Query on GPN
A, B
PEPTIDE-LIKEC11 H16 N7 O4

--

APN
Query on APN
A, B
PEPTIDE-LIKEC11 H16 N7 O3

--

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 = 36.750α = 90.00
b = 44.070β = 91.51
c = 31.220γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
TRUNCATEdata reduction
DENZOdata reduction
CCP4data scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance