Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.61 kDa 
• Atom Count: 413 
• Modelled Residue Count: 18 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

1XJ9

Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network

• PDB DOI: 10.2210/pdb1XJ9/pdb
• NDB: UP0006

• Classification: PEPTIDE NUCLEIC ACID
• Mutation(s): No 


• Deposited: 2004-09-23 Released: 2005-02-22 
• Deposition Author(s): Petersson, B., Nielsen, B.B., Rasmussen, H., Larsen, I.K., Gajhede, M., Nielsen, P.E., Kastrup, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.255 

Literature

Crystal Structure of a Partly Self-Complementary Peptide Nucleic Acid (PNA) Oligomer Showing a Duplex-Triplex Network

Petersson, B., Nielsen, B.B., Rasmussen, H., Larsen, I.K., Gajhede, M., Nielsen, P.E., Kastrup, J.S.

(2005) J Am Chem Soc 127: 1424-1430

• PubMed: 15686374 
• DOI: 10.1021/ja0458726
• Primary Citation of Related Structures:  
  1XJ9


• PubMed Abstract: 
  

The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-l-Lys-NH(2)) to 2.60 A resolution is reported. The structure is mainly controlled by the canonical Watson-Crick base pairs formed by the self-complementary stretch of four bases in the middle of the decamer (G(4)A(5)T(6)C(7)). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C(9)T(10) change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C(9)T(10) allows formation of Hoogsteen hydrogen bonding between C(9)T(10) and G(4)A(5) of a PNA strand in an adjacent Watson-Crick double helix of the same handedness. Thereby, a PNA-PNA-PNA triplex is formed. The PNA unit A(3) forms a noncanonical base pair with A(8) in a symmetry-related strand of opposite handedness; the base pair is of the A-A reverse Hoogsteen type. The structural diversity of this PNA demonstrates how the PNA backbone is able to adapt to structures governed by the stacking and hydrogen-bonding interactions between the nucleobases. The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks.

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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 Biol 4: 98

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)	A, B	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.255 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.6	α = 90
b = 41.9	β = 117.7
c = 30.1	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-23 
• Released Date: 2005-02-22 
Deposition Author(s): Petersson, B., Nielsen, B.B., Rasmussen, H., Larsen, I.K., Gajhede, M., Nielsen, P.E., Kastrup, J.S.

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance