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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.225 (Depositor), 0.249 (DCC)
R-Value Work:
0.176 (Depositor), 0.190 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 Search on PubMed
DOI: https://doi.org/10.1039/b716390h
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.225 (Depositor), 0.249 (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

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Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

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