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 

  • Method: NEUTRON DIFFRACTION

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references