463D | pdb_0000463d

CALCIUM FORM OF D(CGCGAATTCGCG)2

• PDB DOI: https://doi.org/10.2210/pdb463D/pdb
• NAKB: 463D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1999-03-29 Released: 1999-10-08 
• Deposition Author(s): Liu, J., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.257 (Depositor) 
• R-Value Work: 
  0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Structure of d(CGCGAATTCGCG) in the presence of Ca(2+) ions.

Liu, J., Subirana, J.A.

(1999) J Biological Chem 274: 24749-24752

• PubMed: 10455145 
• DOI: https://doi.org/10.1074/jbc.274.35.24749
• Primary Citation of Related Structures:  
  463D


• PubMed Abstract: 
  

  The dodecamer d(CGCGAATTCGCG) was the first oligonucleotide to be crystallized as a B-DNA duplex. Its structure was analyzed in detail in the early 1980s. Here we show that, in the presence of Ca(2+), it crystallizes in a different way (R3 space group). The dodecamers form parallel columns of straight duplexes with ten base pairs in the B form. The terminal cytosines in each molecule are disordered, whereas the terminal guanines are placed in the minor groove of neighbor duplexes. The central GAATTC region is practically identical to that found in the classic structure of the same dodecamer crystallized in the P2(1)2(1)2(1) space group in the presence of Mg(2+) and spermine. Its structure is thus independent of the crystallization conditions which have been used.

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Organizational Affiliation: 

Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Diagonal 647, E-08028, Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.49 kDa 
• Atom Count: 602 
• Modelled Residue Count: 22 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (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], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.257 (Depositor) 
• R-Value Work:  0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.117	α = 90
b = 41.117	β = 90
c = 99.912	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-08 
Deposition Author(s): Liu, J., Subirana, J.A.

Revision History  

• Version 1.0: 1999-10-08
  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