5EYQ | pdb_00005eyq

Racemic crystal structures of Pribnow box consensus promoter sequence (Pnna)

• PDB DOI: https://doi.org/10.2210/pdb5EYQ/pdb
• NAKB: 5EYQ

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


• Deposited: 2015-11-25 Released: 2016-05-18 
• Deposition Author(s): Mandal, P.K., Collie, G.W., Kauffmann, B., Srivastava, S.C., Huc, I.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.357 (Depositor), 0.363 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

Literature

Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.

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

(2016) Nucleic Acids Res 44: 5936-5943

• PubMed: 27137886 
• DOI: https://doi.org/10.1093/nar/gkw367
• Primary Citation Related Structures: 
  5ET9, 5EWB, 5EYQ, 5EZF, 5F26, 5J0E


• PubMed Abstract: 
  

  It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65-2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence.

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Organizational Affiliation: 
• Université de Bordeaux, CBMN (UMR5248), Pessac 33600, France CNRS, CBMN (UMR5248), Pessac 33600, France.
ChemGenes Corporation, 33 Industrial Way, Wilmington, MA 01887, USA.
Université de Bordeaux, Institut Européen de Chimie et Biologie (UMS3033), Pessac 33600, France CNRS, Institut Européen de Chimie et Biologie (UMS3033), Pessac 33600, France INSERM, Institut Européen de Chimie et Biologie (US001), Pessac 33600, France.
Université de Bordeaux, CBMN (UMR5248), Pessac 33600, France CNRS, CBMN (UMR5248), Pessac 33600, France [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.35 kDa 
• Atom Count: 506 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Pribnow box template strand	A	12	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Complementary strand	B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.357 (Depositor), 0.363 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P n n a

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.905	α = 90
b = 68.454	β = 90
c = 34.211	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Mandal, P.K., Collie, G.W., Kauffmann, B., Srivastava, S.C., Huc, I.

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

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Database references
• Version 1.2: 2017-11-29
  Changes: Database references
• Version 1.3: 2018-11-21
  Changes: Data collection, Derived calculations
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description