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 

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This is version 1.3 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 1.75 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-cytochrome b5 reductase
A, B
243Physarum polycephalumMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
IOD
Query on IOD
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
I [auth B]		IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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

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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
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description