1CYO

BOVINE CYTOCHROME B(5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


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.,Sect.D 52: 65-76

  • DOI: 10.1107/S0907444995007827

  • 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 ...

    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 Harbor 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B5
A
93Bos taurusMutation(s): 0 
Gene Names: CYB5A (CYB5)
Find proteins for P00171 (Bos taurus)
Go to Gene View: CYB5A
Go to UniProtKB:  P00171
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.540α = 90.00
b = 46.040β = 90.00
c = 29.910γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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