2RF3 | pdb_00002rf3

Crystal Structure of Tricyclo-DNA: An Unusual Compensatory Change of Two Adjacent Backbone Torsion Angles

• PDB DOI: https://doi.org/10.2210/pdb2RF3/pdb
• NAKB: 2RF3

• Classification: DNA
• Mutation(s): No 


• Deposited: 2007-09-27 Released: 2008-02-12 
• Deposition Author(s): Pallan, P.S., Ittig, D., Heroux, A., Wawrzak, Z., Leumann, C.J., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.225 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tricyclo-DNA: an unusual compensatory change of two adjacent backbone torsion angles.

Pallan, P.S., Ittig, D., Heroux, A., Wawrzak, Z., Leumann, C.J., Egli, M.

(2008) Chem Commun (Camb) 2008: 883-885

• PubMed: 18253536 
• DOI: https://doi.org/10.1039/b716390h
• Primary Citation of Related Structures:  
  2RF3


• PubMed Abstract: 
  

  The crystal structure of a DNA duplex with tricyclo-DNA (tc-DNA) residues explains the increased RNA affinity of tc-DNA relative to DNA and tc-DNA's superior resistance to nucleases.

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Organizational Affiliation: 

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.67 kDa 
• Atom Count: 600 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-d(CGCG(TCY)ATTCGCG)-3'	A, B	12	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.225 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.587	α = 90
b = 26.587	β = 90
c = 98.238	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Pallan, P.S., Ittig, D., Heroux, A., Wawrzak, Z., Leumann, C.J., Egli, M.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description