3M8D

Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

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: 10.1016/j.bpj.2010.06.026
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin B12 transporter btuB
A
594Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: btuB (bfe, cer, dcrC)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
Protein: 
apo BtuB cobalamin transporter
Find proteins for P06129 (Escherichia coli (strain K12))
Go to UniProtKB:  P06129
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

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Download CCD File 
A
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MTN
Query on MTN

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Download CCD File 
A
S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
MTSL
C10 H18 N O3 S2
MXZPGYFBZHBAQM-UHFFFAOYSA-N
 Ligand Interaction
CNC
Query on CNC

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Download CCD File 
A
CO-CYANOCOBALAMIN
C63 H88 Co N14 O14 P
OEEKSCBDGPRZJZ-BYLSPCLQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.051α = 90.00
b = 82.051β = 90.00
c = 224.457γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
MAR345data collection
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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