5CE4

High Resolution X-Ray and Neutron diffraction structure of H-FABP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

    wwPDB Validation   3D Report Full Report


    This is version 1.2 of the entry. See complete history


    Literature

    High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP-oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution.

    Howard, E.I.Guillot, B.Blakeley, M.P.Haertlein, M.Moulin, M.Mitschler, A.Cousido-Siah, A.Fadel, F.Valsecchi, W.M.Tomizaki, T.Petrova, T.Claudot, J.Podjarny, A.

    (2016) IUCrJ 3: 115-126

    • DOI: https://doi.org/10.1107/S2052252515024161
    • Primary Citation of Related Structures:  
      5CE4

    • PubMed Abstract: 

      Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.


    • Organizational Affiliation

      Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France; Instituto de Fisica de Liquidos y Sistemas Biologicos, CONICET, UNLP, Calle 59 No. 789, La Plata, Argentina.


    Macromolecules
    Find similar proteins by:  (by identity cutoff)  |  3D Structure
    Entity ID: 1
    MoleculeChains Sequence LengthOrganismDetailsImage
    Fatty acid-binding protein, heart132Homo sapiensMutation(s): 0 
    Gene Names: FABP3FABP11MDGI
    UniProt & NIH Common Fund Data Resources
    Find proteins for P05413 (Homo sapiens)
    Explore P05413 
    Go to UniProtKB:  P05413
    PHAROS:  P05413
    GTEx:  ENSG00000121769 
    Entity Groups  
    Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
    UniProt GroupP05413
    Sequence Annotations
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChains Name / Formula / InChI Key2D Diagram3D Interactions
    OLA
    Query on OLA

    Download Ideal Coordinates CCD File 
    B [auth A]OLEIC ACID
    C18 H34 O2
    ZQPPMHVWECSIRJ-KTKRTIGZSA-N
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 0.98 Å
    • R-Value Free: 0.159 
    • R-Value Work: 0.139 
    • R-Value Observed: 0.140 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 34.588α = 90
    b = 55.307β = 90
    c = 71.185γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    AMoREphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2016-03-09
      Type: Initial release
    • Version 1.1: 2016-04-06
      Changes: Database references
    • Version 1.2: 2018-11-14
      Changes: Data collection