4YJG | pdb_00004yjg

Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)

PDB DOI: https://doi.org/10.2210/pdb4YJG/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.237 (Depositor), 0.201 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of DAAO variant

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

To be published.

Macromolecule Content

Total Structure Weight: 79.28 kDa
Atom Count: 5,629
Modeled Residue Count: 681
Deposited Residue Count: 681
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino-acid oxidase	A	341	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00371
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00371
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
4DD Query on 4DD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	(2R)-4-phenylbutan-2-amine C₁₀ H₁₅ N WECUIGDEWBNQJJ-SECBINFHSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237 (Depositor), 0.201 (DCC)
R-Value Work: 0.190 (Depositor)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.59	α = 90
b = 92.114	β = 90
c = 110.274	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description