1PUP | pdb_00001pup

CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1PUP/pdb
• NAKB: 1PUP

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


• Deposited: 1996-11-01 Released: 1997-02-25 
• Deposition Author(s): Rasmussen, H., Kastrup, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

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: 98-101

• PubMed: 9033585 
• DOI: https://doi.org/10.1038/nsb0297-98
• Primary Citation Related Structures: 
  1PUP


• PubMed Abstract: 
  

  The crystal structure of a PNA duplex reveals both a right- and a left-handed helix in the unit cell. The helices are wide (28A), large pitched (18bp) with the base pairs perpendicular to the helix axis, thereby demonstrating that PNA besides adapting to oligonucleotide partners also has a unique structure by itself.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.3 kDa 
• Atom Count: 338 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2)	A, B	7	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.97	α = 88.2
b = 26.92	β = 79.4
c = 33.78	γ = 82.5

Software Package:

Software Name	Purpose
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-25 
Deposition Author(s): Rasmussen, H., Kastrup, J.S.

Revision History  

• Version 1.0: 1997-02-25
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2012-03-28
  Changes: Other
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2026-04-01
  Changes: Polymer sequence, Structure summary