2G1Z

X-ray structure of the oligonucleotide sequence d(AAATTT)

• PDB DOI: https://doi.org/10.2210/pdb2G1Z/pdb
• NAKB: 2G1Z

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-02-15 Released: 2006-03-21 
• Deposition Author(s): Valls, N., Santaolalla, A., Campos, J.L., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.380 
• R-Value Work: 0.282 
• R-Value Observed: 0.291 

Literature

Packing features of the all-AT oligonucleotide d(AAATTT).

Valls, N., Santaolalla, A., Campos, J.L., Subirana, J.A.

(2007) J Biomol Struct Dyn 24: 547-552

• PubMed: 17508776 
• DOI: https://doi.org/10.1080/07391102.2007.10507143
• Primary Citation of Related Structures:  
  2G1Z


• PubMed Abstract: 
  

  We describe the packing features of the oligonucleotide duplex d(AAATTT)2, as determined by X-ray diffraction. There is little information on sequences that only contain A and T bases. The present structure confirms that these sequences tend to pack as a helical arrangement of stacked oligonucleotides in a B conformation with Watson-Crick hydrogen bonding. Our results demonstrate that the virtual TA base step between stacked duplexes has a negative twist that improves base stacking. This observation is consistent with the low stability of TA base steps in B-form DNA.

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Organizational Affiliation: 

Departament d'Enginyeria Quimica, Universitat Politecnica de Catalunya, Av. Diagonal 647, E-08028 Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.42 kDa 
• Atom Count: 360 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.380 
• R-Value Work: 0.282 
• R-Value Observed: 0.291 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.127	α = 90
b = 43.127	β = 90
c = 176.579	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Valls, N., Santaolalla, A., Campos, J.L., Subirana, J.A.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-06
  Changes: Data collection, Database references
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references