3DJE | pdb_00003dje

Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II) in complex with FSA

• PDB DOI: https://doi.org/10.2210/pdb3DJE/pdb

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


• Deposited: 2008-06-23 Released: 2008-07-22 
• Deposition Author(s): Collard, F., Zhang, J., Nemet, I., Qanungo, K.R., Monnier, V.M., Yee, V.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.197 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of the deglycating enzyme fructosamine oxidase (FAOX-II)

Collard, F., Zhang, J., Nemet, I., Qanungo, K.R., Monnier, V.M., Yee, V.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.18 kDa 
• Atom Count: 8,096 
• Modeled Residue Count: 873 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructosyl amine: oxygen oxidoreductase	A, B	438	Aspergillus fumigatus	Mutation(s): 0
UniProt
Find proteins for P78573 (Aspergillus fumigatus) Explore P78573  Go to UniProtKB:  P78573

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FSA	D [auth A], F [auth B]	1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose C8 H14 O7 S UORIXTGMSRMKDZ-CCXZUQQUSA-N
EPE	G [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.197 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.143	α = 90
b = 53.436	β = 113.33
c = 103.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Collard, F., Zhang, J., Nemet, I., Qanungo, K.R., Monnier, V.M., Yee, V.C.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary