2A2T | pdb_00002a2t

crystal structure of d(AAATATTT)

• PDB DOI: https://doi.org/10.2210/pdb2A2T/pdb
• NAKB: 2A2T

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-06-23 Released: 2005-11-29 
• Deposition Author(s): Valls, N., Richter, M., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.357 (Depositor), 0.339 (DCC) 
• R-Value Work: 
  0.272 (Depositor) 
• R-Value Observed: 
  0.276 (Depositor) 

Literature

Structure of a DNA duplex with all-AT base pairs.

Valls, N., Richter, M., Subirana, J.A.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1587-1593

• PubMed: 16301792 
• DOI: https://doi.org/10.1107/S0907444905029781
• Primary Citation Related Structures: 
  2A2T


• PubMed Abstract: 
  

  The structure of the oligonucleotide duplex d(AAATATTT)(2) has been obtained in two crystal forms. In both cases the duplexes show Watson-Crick base pairs and are organized as a helical arrangement of stacked oligonucleotides. The helices contain either 11 duplexes in seven turns (form I) or 14 duplexes in nine turns (form II). As a result, the crystals have rather large unit cells. Such an organization of DNA duplexes has not been previously described in oligonucleotide crystal structures. The columns of stacked duplexes are organized in a pseudohexagonal arrangement. They do not show any direct lateral interactions; instead, these are indirectly mediated by shared and disordered hydrated ions. Such interactions are similar to those found in DNA fibres. The structural parameters of the individual base steps coincide with those found in other structures which contain CG terminal base pairs.

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Organizational Affiliation: 
• Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Barclelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.82 kDa 
• Atom Count: 1,823 
• Modeled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'	A, B [auth G], C [auth B], D [auth H], E [auth C], F [auth I], G [auth D], H [auth J], I [auth E], J [auth K], K [auth F]	8	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	R [auth E], S [auth E], T [auth E], U [auth E], V [auth E], W [auth E]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
MN	L [auth D], M [auth E], N [auth E], O [auth E], P [auth E], Q [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.357 (Depositor), 0.339 (DCC) 
• R-Value Work:  0.272 (Depositor) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.623	α = 90
b = 24.985	β = 90.51
c = 82.139	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-29 
Deposition Author(s): Valls, N., Richter, M., Subirana, J.A.

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations