1S2R

A High Resolution Crystal Structure of [d(CGCAAATTTGCG)]2

• PDB DOI: https://doi.org/10.2210/pdb1S2R/pdb
• NAKB: 1S2R

• Classification: DNA
• Mutation(s): No 


• Deposited: 2004-01-09 Released: 2005-01-04 
• Deposition Author(s): Woods, K.K., Maehigashi, T., Howerton, S.B., Tannenbaum, S., Williams, L.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2.

Woods, K.K., Maehigashi, T., Howerton, S.B., Sines, C.C., Tannenbaum, S., Williams, L.D.

(2004) J Am Chem Soc 126: 15330-15331

• PubMed: 15563130 
• DOI: https://doi.org/10.1021/ja045207x
• Primary Citation of Related Structures:  
  1S2R


• PubMed Abstract: 
  

  The crystal structure of [d(CGCAAATTTGCG)]2 has been determined to 1.5 A resolution, representing the first high-resolution structure of this DNA fragment. The ion interactions are novel. A spermine molecule replaces a Mg2+ observed in analogous structures. Unlike lower-resolution structures, the minor groove is narrow and the major groove lacks extra Watson-Crick hydrogen bonds. In addition, a monolayer of solvent sites, including a "spine of hydration", is visible in the minor groove. The crystal of [d(CGCAAATTTGCG)]2 was grown from a solution containing spermine, magnesium, and lithium. The conformation recapitulates that of "monovalent-minus" DNA.

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Organizational Affiliation: 

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.73 kDa 
• Atom Count: 676 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	C [auth A], D [auth B]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.809	α = 90
b = 41.96	β = 90
c = 66.779	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
MOSFLM	data reduction
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-04 
Deposition Author(s): Woods, K.K., Maehigashi, T., Howerton, S.B., Tannenbaum, S., Williams, L.D.

Revision History  

• Version 1.0: 2005-01-04
  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, Derived calculations