9VPF | pdb_00009vpf

Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.

• PDB DOI: https://doi.org/10.2210/pdb9VPF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vanrija humicola
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-03 Released: 2025-10-01 
• Deposition Author(s): Goto, M., Nonaka, R., Mizobuchi, T., Imanishi, D., Takahashi, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.

Goto, M., Nonaka, R., Mizobuchi, T., Imanishi, D., Takahashi, S.

(2025) Acta Crystallogr F Struct Biol Commun 81: 434-440

• PubMed: 40970329 
• DOI: https://doi.org/10.1107/S2053230X25008192
• Primary Citation of Related Structures:  
  9VPF


• PubMed Abstract: 
  

  The enzyme D-aspartate oxidase (DDO) oxidizes acidic D-amino acids using the coenzyme flavin adenine dinucleotide to generate the corresponding α-keto acids and ammonia. DDO differs from D-amino-acid oxidase (DAAO), which acts on neutral and basic D-amino acids. Although the enzymatic properties of DDO have been characterized in several species, the structure of DDO had remained unclear. The structure of DDO derived from Cryptococcus humicola strain UJ1 (chDDO) was determined by X-ray crystallography at 1.70 Å resolution. While the three-dimensional structures of DAAOs are known to be homodimers, chDDO forms a homotetramer. This difference was found to be caused by the deletion of one loop and the insertion of two loops.

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Organizational Affiliation: 
• Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
Department of Material Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 161.2 kDa 
• Atom Count: 12,326 
• Modeled Residue Count: 1,437 
• Deposited Residue Count: 1,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-aspartate oxidase	A, B, C, D	370	Vanrija humicola	Mutation(s): 0  Gene Names: DDO EC: 1.4.3.1
UniProt
Find proteins for Q75WF1 (Vanrija humicola) Explore Q75WF1  Go to UniProtKB:  Q75WF1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], J [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
F	F [auth A], H [auth B]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39VPF

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.983	α = 90
b = 109.338	β = 90
c = 189.401	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Goto, M., Nonaka, R., Mizobuchi, T., Imanishi, D., Takahashi, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP 22770113

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Database references