6GN3

Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group P21/n

• PDB DOI: https://doi.org/10.2210/pdb6GN3/pdb
• NAKB: 6GN3

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


• Deposited: 2018-05-29 Released: 2019-09-11 
• Deposition Author(s): Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.318 
• R-Value Work: 0.280 
• R-Value Observed: 0.284 

Literature

Racemic crystal structures of A-DNA duplexes

Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.31 kDa 
• Atom Count: 751 
• Modelled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')	A, B, C, D, E, F	6	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TMO	G [auth A], H [auth A], J [auth B], M [auth F]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N
CO	I [auth B], L [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.318 
• R-Value Work: 0.280 
• R-Value Observed: 0.284 
• Space Group: P 1 2₁/n 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.883	α = 90
b = 41.43	β = 97.47
c = 71.958	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.

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Funding Organization	Location	Grant Number
European Research Council	France	ERC-2012-AdG-320892

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description