7VKF | pdb_00007vkf

Reduced enzyme of FAD-dpendent Glucose Dehydrogenase complex with D-glucono-1,5-lactone at pH8.5

• PDB DOI: https://doi.org/10.2210/pdb7VKF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-29 Released: 2022-10-05 
• Deposition Author(s): Nakajima, Y., Nishiya, Y., Ito, K.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5

Nakajima, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.93 kDa 
• Atom Count: 4,964 
• Modeled Residue Count: 566 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMC oxidoreductase	A	572	Aspergillus oryzae	Mutation(s): 0  Gene Names: OAory_01010120 EC: 1.1.3.4
UniProt
Find proteins for A0A1S9DW10 (Aspergillus oryzae) Explore A0A1S9DW10  Go to UniProtKB:  A0A1S9DW10

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA (Subject of Investigation/LOI)	C [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
B3P	D [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
LGC (Subject of Investigation/LOI)	B [auth A]	D-glucono-1,5-lactone C6 H10 O6 PHOQVHQSTUBQQK-SQOUGZDYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.421	α = 90
b = 95.421	β = 90
c = 123.841	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Nakajima, Y., Nishiya, Y., Ito, K.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24780106

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Structure summary
• Version 1.2: 2024-05-29
  Changes: Data collection