2DCG | pdb_00002dcg

MOLECULAR STRUCTURE OF A LEFT-HANDED DOUBLE HELICAL DNA FRAGMENT AT ATOMIC RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2DCG/pdb
• NAKB: 2DCG

• Classification: DNA
• Mutation(s): No 


• Deposited: 1988-08-29 Released: 1989-01-09 
• Deposition Author(s): Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., Van Boom, J.H., Van Der Marel, G.A., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Molecular structure of a left-handed double helical DNA fragment at atomic resolution.

Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G., Rich, A.

(1979) Nature 282: 680-686

• PubMed: 514347 
• DOI: https://doi.org/10.1038/282680a0
• Primary Citation Related Structures: 
  2DCG


• PubMed Abstract: 
  

  The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.05 kDa 
• Atom Count: 343 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')	A, B	6	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.87	α = 90
b = 31.55	β = 90
c = 44.58	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1989-01-09 
Deposition Author(s): Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., Van Boom, J.H., Van Der Marel, G.A., Rich, A.

Revision History  

• Version 1.0: 1989-01-09
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations