1DNM | pdb_00001dnm

CRYSTAL STRUCTURE AND SEQUENCE-DEPENDENT CONFORMATION OF THE A.G MIS-PAIRED OLIGONUCLEOTIDE D(CGCAAGCTGGCG)

• PDB DOI: https://doi.org/10.2210/pdb1DNM/pdb
• NAKB: 1DNM

• Classification: DNA
• Mutation(s): No 


• Deposited: 1990-06-22 Released: 1991-07-15 
• Deposition Author(s): Webster, G.D., Sanderson, M.R., Skelly, J.V., Neidle, S., Swann, P.F., Li, B.F., Tickle, I.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).

Webster, G.D., Sanderson, M.R., Skelly, J.V., Neidle, S., Swann, P.F., Li, B.F., Tickle, I.J.

(1990) Proc Natl Acad Sci U S A 87: 6693-6697

• PubMed: 2395870 
• DOI: https://doi.org/10.1073/pnas.87.17.6693
• Primary Citation of Related Structures:  
  1DNM


• PubMed Abstract: 
  

  The crystal structure of the dodecanucleotide d(CGCAAGCTGGCG) has been determined to a resolution of 2.5 A and refined to an R factor of 19.3% for 1710 reflections. The sequence crystallizes as a B-type double helix, with two G(anti).A(syn) base pairs. These are stabilized by three-center hydrogen bonds to pyrimidines that induce perturbations in base-pair geometry. The central AGCT region of the helix has a wide (greater than 6 A) minor groove.

---

Organizational Affiliation: 

Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, United Kingdom.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.38 kDa 
• Atom Count: 537 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.29	α = 90
b = 41.78	β = 90
c = 64.76	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-07-15 
Deposition Author(s): Webster, G.D., Sanderson, M.R., Skelly, J.V., Neidle, S., Swann, P.F., Li, B.F., Tickle, I.J.

Revision History  

• Version 1.0: 1991-07-15
  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: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references