1CYO

BOVINE CYTOCHROME B(5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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This is version 1.3 of the entry. See complete history


Literature

Refinement and structural analysis of bovine cytochrome b5 at 1.5 A resolution.

Durley, R.C.Mathews, F.S.

(1996) Acta Crystallogr D Biol Crystallogr 52: 65-76

  • DOI: 10.1107/S0907444995007827
  • Primary Citation of Related Structures:  
    1CYO

  • PubMed Abstract: 
  • The structure of bovine liver cytochrome b(5), a soluble 93-residue proteolytic fragment of a 16 kDa membrane-bound hemoprotein, initially solved at 2.0 A resolution, has been refined at 1.5 A using data collected on a diffractometer. Refinement to 2.0 A resolution used the Hendrickson-Konnert procedure PROLSQ and was then extended to 1 ...

    The structure of bovine liver cytochrome b(5), a soluble 93-residue proteolytic fragment of a 16 kDa membrane-bound hemoprotein, initially solved at 2.0 A resolution, has been refined at 1.5 A using data collected on a diffractometer. Refinement to 2.0 A resolution used the Hendrickson-Konnert procedure PROLSQ and was then extended to 1.5 A resolution using the program PROFFT. Only residues 3-87 could be identified in the model and these residues together with 93 water molecules gave an agreement factor of R = 0.161 for data in the resolution range 1.5-5 A. The structure was finally refined using the program X-PLOR, which enabled alternate conformers to be modelled for several surface side chains. Residues 1 and 2 at the amino terminus of the protein and residue 88 near the carboxyl terminus could be identified from these electron-density maps. However the remaining disordered carboxy-terminal residues could not successfully be included in the model. A total of 117 solvent molecules were included in the final refinement to give R = 0.164 for the data between 1.5 and 10 A.


    Related Citations: 
    • Cytochrome B5 and Cytochrome B5 Reductase from a Chemical and X-Ray Diffraction Viewpoint
      Mathews, F.S., Czerwinski, E.W.
      (1985) The Enzymes Of Biological Membranes 2nd Ed V 4: Bioenergetics Of Electron And Proton Transport 4: 235
    • The X-Ray Crystallographic Structure of Calf Liver Cytochrome B5
      Mathews, F.S., Czerwinski, E.W., Argos, P.
      (1979) The Porphyrins V 7: Biochemistry, Pt B 7: 107
    • The Structure of Cytochrome B5 at 2.0 Angstroms Resolution
      Mathews, F.S., Argos, P., Levine, M.
      (1972) Cold Spring Harb Symp Quant Biol 36: 387

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B5A93Bos taurusMutation(s): 0 
Gene Names: CYB5ACYB5
UniProt
Find proteins for P00171 (Bos taurus)
Explore P00171 
Go to UniProtKB:  P00171
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.54α = 90
b = 46.04β = 90
c = 29.91γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other