8HDD

Complex structure of catalytic, small, and a partial electron transfer subunits from Burkholderia cepacia FAD glucose dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb8HDD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia cepacia
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-11-04 Released: 2022-12-14 
• Deposition Author(s): Yoshida, H., Sode, K.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.323 
• R-Value Work: 0.275 
• R-Value Observed: 0.278 

Literature

Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase

Okuda-Shimazaki, J., Yoshida, H., Lee, I., Kojima, K., Suzuki, N., Tsugawa, W., Yamada, M., Inaka, K., Tanaka, H., Sode, K.

(2022) Commun Biol 5: 1334

• DOI: https://doi.org/10.1038/s42003-022-04286-9

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126.46 kDa 
• Atom Count: 6,037 
• Modelled Residue Count: 768 
• Deposited Residue Count: 1,142 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose dehydrogenase	A	539	Burkholderia cepacia	Mutation(s): 0  Gene Names: gdhAlpha EC: 1.1.5.9
UniProt
Find proteins for Q8GQE7 (Burkholderia cepacia) Explore Q8GQE7  Go to UniProtKB:  Q8GQE7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose dehydrogenase beta subunit	B	482	Burkholderia cepacia	Mutation(s): 2
UniProt
Find proteins for Q71JE9 (Burkholderia cepacia) Explore Q71JE9  Go to UniProtKB:  Q71JE9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation pathway signal	C	121	Burkholderia cepacia	Mutation(s): 0  Gene Names: BMULJ_04411
UniProt
Find proteins for A0A0H3KLY3 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KLY3  Go to UniProtKB:  A0A0H3KLY3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM (Subject of Investigation/LOI)	F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
F3S (Subject of Investigation/LOI)	E [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.323 
• R-Value Work: 0.275 
• R-Value Observed: 0.278 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.015	α = 90
b = 71.797	β = 90
c = 114.221	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data reduction
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Yoshida, H., Sode, K.

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Funding Organization	Location	Grant Number
Other private	Japan	NA (sponsorship research)

Revision History  

• Version 1.0: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description