5GV7

Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.80 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase.

Takaba, K.Takeda, K.Kosugi, M.Tamada, T.Miki, K.

(2017) Sci Rep 7: 43162-43162

  • DOI: 10.1038/srep43162
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence e ...

    Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b5 reductase (b5R), at an ultra-high resolution of 0.78 Å. Valence electrons on the FAD cofactor as well as the peptide portion, which are clearly visualized even after the conventional refinement, are analyzed by the multipolar atomic model refinement. The topological analysis for the determined electron density reveals the valence electronic structure of the isoalloxazine ring of FAD and hydrogen-bonding interactions with the protein environment. The tetrahedral electronic distribution around the N5 atom of FAD in b5R is stabilized by hydrogen bonding with CαH of Tyr65 and amide-H of Thr66. The hydrogen bonding network leads to His49 composing the cytochrome b5-binding site via non-classical hydrogen bonds between N5 of FAD and CαH of Tyr65 and O of Tyr65 and CβH of His49.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-cytochrome b5 reductase 3
A
272Sus scrofaMutation(s): 0 
Gene Names: CYB5R3 (DIA1)
EC: 1.6.2.2
Find proteins for P83686 (Sus scrofa)
Go to Gene View: CYB5R3
Go to UniProtKB:  P83686
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.122 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.664α = 90.00
b = 72.177β = 90.00
c = 85.209γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Data collection, Refinement description