1ZYT

Crystal structure of spin labeled T4 Lysozyme (A82R1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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    Ligand Structure Quality Assessment 


    This is version 1.4 of the entry. See complete history


    Literature

    Structural origin of weakly ordered nitroxide motion in spin-labeled proteins

    Fleissner, M.R.Cascio, D.Hubbell, W.L.

    (2009) Protein Sci 18: 893-908

    • DOI: https://doi.org/10.1002/pro.96
    • Primary Citation of Related Structures:  
      1ZYT, 2CUU, 3G3V, 3G3W, 3G3X

    • PubMed Abstract: 

      A disulfide-linked nitroxide side chain (R1) used in site-directed spin labeling of proteins often exhibits an EPR spectrum characteristic of a weakly ordered z-axis anisotropic motion at topographically diverse surface sites, including those on helices, loops and edge strands of beta-sheets. To elucidate the origin of this motion, the first crystal structures of R1 that display simple z-axis anisotropic motion at solvent-exposed helical sites (131 and 151) and a loop site (82) in T4 lysozyme have been determined. Structures of 131R1 and 151R1 determined at cryogenic or ambient temperature reveal an intraresidue C(alpha)--H...S(delta) interaction that immobilizes the disulfide group, consistent with a model in which the internal motions of R1 are dominated by rotations about the two terminal bonds (Columbus, Kálai, Jeko, Hideg, and Hubbell, Biochemistry 2001;40:3828-3846). Remarkably, the 131R1 side chain populates two rotamers equally, but the EPR spectrum reflects a single dominant dynamic population, showing that the two rotamers have similar internal motion determined by the common disulfide-backbone interaction. The anisotropic motion for loop residue 82R1 is also accounted for by a common disulfide-backbone interaction, showing that the interaction does not require a specific secondary structure. If the above observations prove to be general, then significant variations in order and rate for R1 at noninteracting solvent-exposed helical and loop sites can be assigned to backbone motion because the internal motion is essentially constant.


    • Organizational Affiliation

      Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-7008.


    Macromolecules
    Find similar proteins by:  (by identity cutoff)  |  3D Structure
    Entity ID: 1
    MoleculeChains Sequence LengthOrganismDetailsImage
    Lysozyme164Tequatrovirus T4Mutation(s): 3 
    EC: 3.2.1.17
    UniProt
    Find proteins for P00720 (Enterobacteria phage T4)
    Explore P00720 
    Go to UniProtKB:  P00720
    Entity Groups  
    Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
    UniProt GroupP00720
    Sequence Annotations
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChains Name / Formula / InChI Key2D Diagram3D Interactions
    MTN
    Query on MTN

    Download Ideal Coordinates CCD File 
    B [auth A]S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
    C10 H18 N O3 S2
    MXZPGYFBZHBAQM-UHFFFAOYSA-N
    HED
    Query on HED

    Download Ideal Coordinates CCD File 
    G [auth A]2-HYDROXYETHYL DISULFIDE
    C4 H10 O2 S2
    KYNFOMQIXZUKRK-UHFFFAOYSA-N
    AZI
    Query on AZI

    Download Ideal Coordinates CCD File 
    C [auth A]AZIDE ION
    N3
    IVRMZWNICZWHMI-UHFFFAOYSA-N
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    D [auth A],
    E [auth A],
    F [auth A]
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.70 Å
    • R-Value Free: 0.206 
    • R-Value Work: 0.186 
    • R-Value Observed: 0.187 
    • Space Group: P 32 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 60.293α = 90
    b = 60.293β = 90
    c = 96.079γ = 120
    Software Package:
    Software NamePurpose
    REFMACrefinement
    DENZOdata reduction
    SCALEPACKdata 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: 2006-08-15
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2011-07-27
      Changes: Non-polymer description
    • Version 1.4: 2023-10-25
      Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description