1D59

CRYSTAL STRUCTURE OF 4-STRANDED OXYTRICHA TELOMERIC DNA

• PDB DOI: https://doi.org/10.2210/pdb1D59/pdb
• NAKB: 1D59

• Classification: DNA
• Mutation(s): No 


• Deposited: 1992-02-25 Released: 1993-04-15 
• Deposition Author(s): Kang, C., Zhang, X., Ratliff, R., Moyzis, R., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Crystal structure of four-stranded Oxytricha telomeric DNA.

Kang, C., Zhang, X., Ratliff, R., Moyzis, R., Rich, A.

(1992) Nature 356: 126-131

• PubMed: 1545863 
• DOI: https://doi.org/10.1038/356126a0
• Primary Citation of Related Structures:  
  1D59


• PubMed Abstract: 
  

  The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.22 kDa 
• Atom Count: 1,012 
• Modelled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.73	α = 90
b = 49.57	β = 90
c = 97.27	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-04-15 
Deposition Author(s): Kang, C., Zhang, X., Ratliff, R., Moyzis, R., Rich, A.

Revision History  

• Version 1.0: 1993-04-15
  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: 2024-02-07
  Changes: Data collection, Database references