5INJ

Crystal Structure of Prenyltransferase PriB Ternary Complex with L-Tryptophan and Dimethylallyl thiolodiphosphate (DMSPP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history


Literature

Structure and specificity of a permissive bacterial C-prenyltransferase.

Elshahawi, S.I.Cao, H.Shaaban, K.A.Ponomareva, L.V.Subramanian, T.Farman, M.L.Spielmann, H.P.Phillips, G.N.Thorson, J.S.Singh, S.

(2017) Nat Chem Biol 13: 366-368

  • DOI: https://doi.org/10.1038/nchembio.2285
  • Primary Citation of Related Structures:  
    5INJ, 5JXM, 5K9M

  • PubMed Abstract: 

    This study highlights the biochemical and structural characterization of the L-tryptophan C6 C-prenyltransferase (C-PT) PriB from Streptomyces sp. RM-5-8. PriB was found to be uniquely permissive to a diverse array of prenyl donors and acceptors including daptomycin. Two additional PTs also produced novel prenylated daptomycins with improved antibacterial activities over the parent drug.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prenyltransferase405Streptomyces sp. RM-5-8Mutation(s): 0 
UniProt
Find proteins for A0A182DWE5 (Streptomyces sp. RM-5-8)
Explore A0A182DWE5 
Go to UniProtKB:  A0A182DWE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A182DWE5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.396α = 90
b = 83.422β = 106.74
c = 41.618γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA84374
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR000117

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2017-03-29
    Changes: Database references
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.2: 2020-09-23
    Changes: Structure summary
  • Version 2.3: 2024-03-06
    Changes: Data collection, Database references