4LX5

X-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.

Robinson, C.J.Vincent, H.A.Wu, M.C.Lowe, P.T.Dunstan, M.S.Leys, D.Micklefield, J.

(2014) J Am Chem Soc 136: 10615-10624

  • DOI: https://doi.org/10.1021/ja502873j
  • Primary Citation of Related Structures:  
    4LX5, 4LX6

  • PubMed Abstract: 

    Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tunable activation or repression of target gene expression, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, while providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes.


  • Organizational Affiliation

    School of Chemistry, ‡Manchester Institute of Biotechnology and §Faculty of Life Sciences, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Mutated adenine riboswitch aptamer71Vibrio vulnificus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.05α = 90
b = 149.71β = 90
c = 24.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description