1RSB

X-ray study of the DNA oligomer d(ATATAT) in P65 space group

• PDB DOI: https://doi.org/10.2210/pdb1RSB/pdb
• NAKB: 1RSB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2003-12-09 Released: 2004-05-25 
• Deposition Author(s): Abrescia, N.G., Gonzalez, C., Gouyette, C., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.263 
• R-Value Work: 0.218 

Literature

X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA.

Abrescia, N.G., Gonzalez, C., Gouyette, C., Subirana, J.A.

(2004) Biochemistry 43: 4092-4100

• PubMed: 15065851 
• DOI: https://doi.org/10.1021/bi0355140
• Primary Citation of Related Structures:  
  1RSB


• PubMed Abstract: 
  

  We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA.

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Organizational Affiliation: 

Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Av. Diagonal 647, E-08028 Barcelona, Spain. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.23 kDa 
• Atom Count: 476 
• Modelled Residue Count: 23 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*AP*TP*AP*T)-3'	A, B, C, D	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.263 
• R-Value Work: 0.218 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.313	α = 90
b = 32.313	β = 90
c = 117.779	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Abrescia, N.G., Gonzalez, C., Gouyette, C., Subirana, J.A.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references