399D

STRUCTURE OF D(CGCCCGCGGGCG)

• PDB DOI: https://doi.org/10.2210/pdb399D/pdb
• NAKB: 399D

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 1998-05-11 Released: 1999-01-18 
• Deposition Author(s): Malinina, L., Fernandez, L.G., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Literature

Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features.

Malinina, L., Fernandez, L.G., Huynh-Dinh, T., Subirana, J.A.

(1999) J Mol Biol 285: 1679-1690

• PubMed: 9917405 
• DOI: https://doi.org/10.1006/jmbi.1998.2424
• Primary Citation of Related Structures:  
  399D


• PubMed Abstract: 
  

  We have determined the structure of the dodecamer duplex d(CGCCCGCGGGCG)2. A careful use of the molecular replacement programme AMoRe has been essential in order to solve the structure. This dodecamer shows a unique conformation, quite different from all the previously studied oligonucleotide duplexes: the central octamer has an A conformation, but with a sharp 65 degrees kink in the centre; the terminal base-steps have a B-like conformation; the major groove is completely closed in the centre, a hollow molecule is thus found. The results obtained confirm the high degree of variability of DNA structure. A new type of kink and an intermediate A/B double-helical conformation have been found. Such intermediate conformation differs from those described in DNA polymerase complexes.

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Organizational Affiliation: 

Departament d'Enginyeria Química, E.T.S.E.I.B., Av. Diagonal 647, Barcelona, 08028, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.33 kDa 
• Atom Count: 549 
• 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*CP*CP*GP*CP*GP*GP*GP*CP*G)-3')	A, B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.29	α = 90
b = 42.602	β = 90
c = 45.995	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-18 
Deposition Author(s): Malinina, L., Fernandez, L.G., Subirana, J.A.

Revision History  

• Version 1.0: 1999-01-18
  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: 2017-05-03
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references