7MJV

MiaB in the complex with s-adenosylmethionine and RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB

Esakova, O.A.Grove, T.L.Yennawar, N.H.Arcinas, A.J.Wang, B.Krebs, C.Almo, S.C.Booker, S.J.

(2021) Nature 


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthaseA457Bacteroides uniformisMutation(s): 0 
Gene Names: 
EC: 2.8.4.3
UniProt
Find proteins for A0A174NUT3 (Bacteroides uniformis)
Explore A0A174NUT3 
Go to UniProtKB:  A0A174NUT3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*GP*GP*AP*CP*UP*GP*AP*AP*(ZJS)P*AP*UP*CP*CP*U)-3')B [auth E]17Bacteroides uniformis
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAM (Subject of Investigation/LOI)
    Query on SAM

    Download Ideal Coordinates CCD File 
    E [auth A]S-ADENOSYLMETHIONINE
    C15 H22 N6 O5 S
    MEFKEPWMEQBLKI-FCKMPRQPSA-N
     Ligand Interaction
    SF4 (Subject of Investigation/LOI)
    Query on SF4

    Download Ideal Coordinates CCD File 
    D [auth A]IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC
     Ligand Interaction
    F3S (Subject of Investigation/LOI)
    Query on F3S

    Download Ideal Coordinates CCD File 
    C [auth A]FE3-S4 CLUSTER
    Fe3 S4
    FCXHZBQOKRZXKS-MZMDZPPWAW
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    F [auth A], G [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.24 Å
    • R-Value Free: 0.273 
    • R-Value Work: 0.243 
    • R-Value Observed: 0.246 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 54.155α = 90
    b = 81.442β = 90
    c = 109.751γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    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 StatesNIH (GM-122595 to S.J.B)
    National Science Foundation (NSF, United States)United StatesNSF (MCB-1716686 to S.J.B.)
    Howard Hughes Medical Institute (HHMI)United StatesSquire J. Booker

    Revision History  (Full details and data files)

    • Version 1.0: 2021-09-15
      Type: Initial release