4II9

Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors

Fonvielle, M.Li de La Sierra-Gallay, I.El-Sagheer, A.H.Lecerf, M.Patin, D.Mellal, D.Mayer, C.Blanot, D.Gale, N.Brown, T.van Tilbeurgh, H.Etheve-Quelquejeu, M.Arthur, M.

(2013) Angew Chem Int Ed Engl 52: 7278-7281


Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FemXA343Weissella viridescensMutation(s): 0 
Gene Names: femX
EC: 2.3.2.10
UniProt
Find proteins for Q9EY50 (Weissella viridescens)
Explore Q9EY50 
Go to UniProtKB:  Q9EY50
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5-mer peptideB5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*CP*CP*(A9Z))-3')C3N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    UDP (Subject of Investigation/LOI)
    Query on UDP

    Download Ideal Coordinates CCD File 
    E [auth B]URIDINE-5'-DIPHOSPHATE
    C9 H14 N2 O12 P2
    XCCTYIAWTASOJW-XVFCMESISA-N
     Ligand Interaction
    MUB (Subject of Investigation/LOI)
    Query on MUB

    Download Ideal Coordinates CCD File 
    F [auth B]N-acetyl-alpha-muramic acid
    C11 H19 N O8
    MNLRQHMNZILYPY-MDMHTWEWSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    D [auth A]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.66 Å
    • R-Value Free: 0.209 
    • R-Value Work: 0.175 
    • R-Value Observed: 0.177 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 42.13α = 90
    b = 101.77β = 102.6
    c = 46.32γ = 90
    Software Package:
    Software NamePurpose
    MXdata collection
    PHASERphasing
    REFMACrefinement
    XDSdata reduction
    XSCALEdata scaling

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-07-03
      Type: Initial release
    • Version 1.1: 2013-08-07
      Changes: Database references
    • Version 2.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary