Crystal structure of spin-labeled BtuB V10R1 in the apo state

Experimental Data Snapshot

  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Conformational exchange in a membrane transport protein is altered in protein crystals.

Freed, D.M.Horanyi, P.S.Wiener, M.C.Cafiso, D.S.

(2010) Biophys J 99: 1604-1610

  • DOI: https://doi.org/10.1016/j.bpj.2010.06.026
  • Primary Citation of Related Structures:  
    3M8B, 3M8D

  • PubMed Abstract: 

    Successful macromolecular crystallography requires solution conditions that may alter the conformational sampling of a macromolecule. Here, site-directed spin labeling is used to examine a conformational equilibrium within BtuB, the Escherichia coli outer membrane transporter for vitamin B(12). Electron paramagnetic resonance (EPR) spectra from a spin label placed within the N-terminal energy coupling motif (Ton box) of BtuB indicate that this segment is in equilibrium between folded and unfolded forms. In bilayers, substrate binding shifts this equilibrium toward the unfolded form; however, EPR spectra from this same spin-labeled mutant indicate that this unfolding transition is blocked in protein crystals. Moreover, crystal structures of this spin-labeled mutant are consistent with the EPR result. When the free energy difference between substates is estimated from the EPR spectra, the crystal environment is found to alter this energy by 3 kcal/mol when compared to the bilayer state. Approximately half of this energy change is due to solutes or osmolytes in the crystallization buffer, and the remainder is contributed by the crystal lattice. These data provide a quantitative measure of how a conformational equilibrium in BtuB is modified in the crystal environment, and suggest that more-compact, less-hydrated substates will be favored in protein crystals.

  • Organizational Affiliation

    Departments of Chemistry, University of Virginia, Charlottesville, Virginia, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin B12 transporter btuB594Escherichia coliMutation(s): 0 
Gene Names: btuBbfecerdcrCb3966JW3938
Membrane Entity: Yes 
Find proteins for P06129 (Escherichia coli (strain K12))
Explore P06129 
Go to UniProtKB:  P06129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06129
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C8E

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
C16 H34 O5
Query on MTN

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I [auth A]S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
C10 H18 N O3 S2
Query on MG

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.29α = 90
b = 81.29β = 90
c = 226.562γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Non-polymer description
  • Version 1.3: 2011-10-26
    Changes: Database references
  • Version 1.4: 2012-02-15
    Changes: Derived calculations, Non-polymer description
  • Version 1.5: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.6: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description