2EIX

The Structure of Physarum polycephalum cytochrome b5 reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of Physarum polycephalum cytochrome b5 reductase at 1.56 A resolution.

Kim, S.Suga, M.Ogasahara, K.Ikegami, T.Minami, Y.Yubisui, T.Tsukihara, T.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 274-279

  • DOI: https://doi.org/10.1107/S1744309107010731
  • Primary Citation of Related Structures:  
    2EIX

  • PubMed Abstract: 
  • Physarum polycephalum cytochrome b(5) reductase catalyzes the reduction of cytochrome b(5) by NADH. The structure of P. polycephalum cytochrome b(5) reductase was determined at a resolution of 1.56 A. The molecular structure was compared with that of human cytochrome b(5) reductase, which had previously been determined at 1 ...

    Physarum polycephalum cytochrome b(5) reductase catalyzes the reduction of cytochrome b(5) by NADH. The structure of P. polycephalum cytochrome b(5) reductase was determined at a resolution of 1.56 A. The molecular structure was compared with that of human cytochrome b(5) reductase, which had previously been determined at 1.75 A resolution [Bando et al. (2004), Acta Cryst. D60, 1929-1934]. The high-resolution structure revealed conformational differences between the two enzymes in the adenosine moiety of the FAD, the lid region and the linker region. The structural properties of both proteins were inspected in terms of hydrogen bonding, ion pairs, accessible surface area and cavity volume. The differences in these structural properties between the two proteins were consistent with estimates of their thermostabilities obtained from differential scanning calorimetry data.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-cytochrome b5 reductaseA, B243Physarum polycephalumMutation(s): 0 
Gene Names: b5R
EC: 1.6.2.2
UniProt
Find proteins for Q1HA49 (Physarum polycephalum)
Explore Q1HA49 
Go to UniProtKB:  Q1HA49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1HA49
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.084α = 90
b = 136.369β = 90
c = 45.718γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance