426D

THE STRUCTURE OF MOST STUDIED DNA FRAGMENT CHANGES UNDER THE INFLUENCE OF IONS: A NEW PACKING OF D(CGCGAATTCGCG)

• PDB DOI: https://doi.org/10.2210/pdb426D/pdb
• NAKB: 426D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-09-17 Released: 1998-11-30 
• Deposition Author(s): Liu, J., Malinina, L., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

The structure of the most studied DNA fragment changes under the influence of ions: a new packing of d(CGCGAATTCGCG).

Liu, J., Malinina, L., Huynh-Dinh, T., Subirana, J.A.

(1998) FEBS Lett 438: 211-214

• PubMed: 9827547 
• DOI: https://doi.org/10.1016/s0014-5793(98)01295-2
• Primary Citation of Related Structures:  
  426D


• PubMed Abstract: 
  

  The title oligonucleotide and many related dodecamers have been extensively studied alone and as DNA-drug complexes. In practically all cases they were found to crystallize in the same space group, stabilized by interactions among the terminal guanine bases. Here we report new packing interactions (R3) in the presence of Ca2+. The oligonucleotides interact by placing their terminal guanines in the narrow groove of a neighbor molecule, an interaction which had never been found in dodecamers.

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Organizational Affiliation: 

Department d'Enginyeria Química, Universitat Politènica de Catalunya, Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.37 kDa 
• Atom Count: 466 
• Modelled Residue Count: 22 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.96	α = 90
b = 41.96	β = 90
c = 101.4	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-30 
Deposition Author(s): Liu, J., Malinina, L., Subirana, J.A.

Revision History  

• Version 1.0: 1998-11-30
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations