4R4D

Racemic crystal structure of a magnesium-bound B-DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb4R4D/pdb
• NAKB: 4R4D

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


• Deposited: 2014-08-19 Released: 2014-11-12 
• Deposition Author(s): Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.311 
• R-Value Work: 0.269 
• R-Value Observed: 0.271 

Literature

Racemic DNA crystallography.

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

(2014) Angew Chem Int Ed Engl 53: 14424-14427

• PubMed: 25358289 
• DOI: https://doi.org/10.1002/anie.201409014
• Primary Citation of Related Structures:  
  4R44, 4R45, 4R47, 4R48, 4R49, 4R4A, 4R4D


• PubMed Abstract: 
  

  Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.

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Organizational Affiliation: 

Université de Bordeaux, CBMN, UMR5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600 Pessac (France); CNRS, CBMN, UMR5248.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.4 kDa 
• Atom Count: 1,111 
• Modelled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'	A, B, C, D	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.311 
• R-Value Work: 0.269 
• R-Value Observed: 0.271 
• Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.61	α = 70.76
b = 32.951	β = 80.77
c = 46.25	γ = 73.77

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description