1U9M

Crystal structure of F58W mutant of cytochrome b5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure of the F58W mutant of cytochrome b5: the mutation leads to multiple conformations and weakens stacking interactions.

Shan, L.Lu, J.X.Gan, J.H.Wang, Y.H.Huang, Z.X.Xia, Z.X.

(2005) Acta Crystallogr D Biol Crystallogr 61: 180-189

  • DOI: https://doi.org/10.1107/S0907444904031798
  • Primary Citation of Related Structures:  
    1U9M, 1U9U

  • PubMed Abstract: 

    Phe58 of cytochrome b5 is involved in stacking interactions with heme and the axial ligand His63. To elucidate the contribution of the stacking interactions to protein stability, the crystal structures of the F58Y and F58W mutants were determined at high resolution. The structure of the F58Y mutant is basically the same as that of the wild-type protein. However, the mutation from Phe58 to Trp58 leads to difficulty in growing single crystals and results in a space-group change; the six molecules in the asymmetric unit form two groups that are related by a non-crystallographic twofold axis. The structure of F58W was determined using molecular replacement by making use of the non-crystallographic symmetry. The F58W mutation gives rise to multiple conformations of six side chains, a peptide linking two of the six residues and the extended propionic acid of the heme. The six molecules in the asymmetric unit of the F58W mutant structure are grouped into two types based on their conformations and one of the six molecules exhibits dual conformations. The stacking interactions are weakened owing to the increase/decrease of the angles between the indole ring of Trp58 and the His63/heme rings, which accounts for the lower stability of F58W compared with the wild-type protein.


  • Organizational Affiliation

    State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b5
A, B, C, D, E
A, B, C, D, E, F
82Bos taurusMutation(s): 1 
UniProt
Find proteins for P00171 (Bos taurus)
Explore P00171 
Go to UniProtKB:  P00171
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00171
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.044α = 90
b = 87.484β = 90
c = 138.383γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description