1LLS

CRYSTAL STRUCTURE OF UNLIGANDED MALTOSE BINDING PROTEIN WITH XENON


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DETECTION AND CHARACTERIZATION OF XENON-BINDING SITES IN PROTEINS BY 129XE NMR SPECTROSCOPY

Rubin, S.M.Lee, S.-Y.Ruiz, E.J.Pines, A.Wemmer, D.E.

(2002) J.MOL.BIOL. 322: 425-440


  • PubMed Abstract: 
  • Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe ...

    Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe chemical shift to its local environment and the intense signals attainable by optical pumping make xenon a useful NMR reporter of its own interactions with proteins. A method for detecting specific xenon-binding interactions by analysis of 129Xe chemical shift data is illustrated using the maltose binding protein (MBP) from Escherichia coli as an example. The crystal structure of MBP in the presence of 8atm of xenon confirms the binding site determined from NMR data. Changes in the structure of the xenon-binding cavity upon the binding of maltose by the protein can account for the sensitivity of the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in solution with a number of cavity containing phage T4 lysozyme mutants show that xenon can report on cavity structure. In particular, a correlation exists between cavity size and the binding-induced 129Xe chemical shift. Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered.


    Related Citations: 
    • Detection of a Conformational Change in Maltose Binding Protein by 129Xe Nuclear Magnetic Resonance
      Rubin, S.M.,Spence, M.M.,Dimitrov, I.E.,Ruiz, E.J.,Pines, A.,Wemmer, D.E.
      (2001) J.Am.Chem.Soc. 123: 8616
    • Crystallographic Evidence of a Large Ligand-Induced Hinge-Twist Motion Between the Two Domains of the Maltodextrin Binding Protein Involved in Active Transport and Chemotaxis
      Sharff, A.J.,Rodseth, L.E.,Spurlino, J.C.,Quiocho, F.A.
      (1992) Biochemistry 31: 10657
    • Size Versus Polarizability in Protein-Ligand Interactions: Binding of Noble Gases within Engineered Cavities in Phage T4 Lysozyme
      Quillin, M.L.,Breyer, W.A.,Griswold, I.J.,Matthews, B.W.
      (2000) J.Mol.Biol. 302: 955
    • The 2.3 A Structure of the Malto- or Maltodextrin-Binding Protein, a Primary Receptor of Bacterial Active Transport
      Spurlino, J.C.,Lu, G.-Y.,Quiocho, F.A.
      (1991) J.Biol.Chem. 266: 5202


    Organizational Affiliation

    Department of Chemistry, MC-1460, University of California, Berkeley 94720-1460, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein
A
370Escherichia coli (strain K12)Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XE
Query on XE

Download SDF File 
Download CCD File 
A
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.207α = 100.75
b = 44.026β = 101.36
c = 57.649γ = 102.62
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance