4YJH

Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form)

• PDB DOI: https://doi.org/10.2210/pdb4YJH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-03-03 Released: 2016-04-06 
• Deposition Author(s): Nakano, S., Yasukawa, K., Kawahara, N., Ishitsubo, E., Tokiwa, H., Asano, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.263 
• R-Value Work: 0.192 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Crystal structure of DAAO variant

Nakano, S., Yasukawa, K., Kawahara, N., Ishitsubo, E., Tokiwa, H., Asano, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 79.22 kDa 
• Atom Count: 5,604 
• Modelled Residue Count: 682 
• Deposited Residue Count: 682 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino-acid oxidase	A	342	Sus scrofa	Mutation(s): 2  Gene Names: DAO EC: 1.4.3.3
UniProt
Find proteins for P00371 (Sus scrofa) Explore P00371  Go to UniProtKB:  P00371

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino-acid oxidase	B	340	Sus scrofa	Mutation(s): 2  Gene Names: DAO EC: 1.4.3.3
UniProt
Find proteins for P00371 (Sus scrofa) Explore P00371  Go to UniProtKB:  P00371

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
96B	C [auth A], F [auth B]	(2R)-2-phenylpyrrolidine C10 H13 N JUTDHSGANMHVIC-SNVBAGLBSA-N
SO4	E [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.263 
• R-Value Work: 0.192 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.281	α = 90
b = 91.202	β = 90
c = 110.007	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Nakano, S., Yasukawa, K., Kawahara, N., Ishitsubo, E., Tokiwa, H., Asano, Y.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description