SAXSdb — 2yr5

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pro-enzyme of L-phenylalanine oxidase

Pseudomonas sp. P-501

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5W9R9_9PSED
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–713； UniProt 2–714 Author chain B； PDBConstruct 1–713； UniProt 2–714

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2yr5
Deposition date deposition_date	2007-04-02
Structure title title	Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501
Keywords keywords	L-phenylalanine oxidase, amino oxidase, flavoenzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2yr5__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2yr5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yr5__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.47 Å
Rg (electron density)	30.45 Å
Total Rg	31.25 Å
Atom count	10574
Residues	1368
Excluded volume	187110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yr5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Pro-enzyme of L-phenylalanine oxidase
Molecular weight formula_weight	77899.7 kDa
EC 编号 ec_number	1.13.12.9
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12783

GVTVIPRLLGLKDEKKIATTVGEARLSGINYRHPDSALVSYPVAAAAPLGRLPAGNYRIAIVGGGAGGIAALYELGRLAATLPAGSGIDVQIYEADPDSFLHDRPGIKAIKVRGLKAGRVSAALVHNGDPASGDTIYEVGAMRFPEIAGLTWHYASAAFGDAAPIKVFPNPGKVPTEFVFGNRVDRYVGSDPKDWEDPDSPTLKVLGVVAGGLVGNPQGENVAMYPIANVDPAKIAAILNAATPPADALERIQTKYWPEFIAQYDGLTLGAAVREIVTVAFEKGTLPPVDGVLDVDESISYYVELFGRFGFGTGGFKPLYNISLVEMMRLILWDYSNEYTLPVTENVEFIRNLFLKAQNVGAGKLVVQVRQERVANACHSGTASARAQLLSYDSHNAVHSEAYDFVILAVPHDQLTPIVSRSGFEHAASQNLGDAGLGLETHTYNQVYPPLLLSDSSPAANARIVTAIGQLHMARSSKVFATVKTAALDQPWVPQWRGEPIKAVVSDSGLAASYVVPSPIVEDGQAPEYSSLLASYTWEDDSTRLRHDFGLYPQNPATETGTADGMYRTMVNRAYRYVKYAGASNAQPWWFYQLLAEARTADRFVFDWTTNKTAGGFKLDMTGDHHQSNLCFRYHTHALAASLDNRFFIASDSYSHLGGWLEGAFMSALNAVAGLIVRANRGDVSALSTEARPLVIGLRPVVKVPAAELATSQLEHHHHHH

Source Source

Source organism organism	Pseudomonas sp. P-501
NCBI taxonomy ID ncbi_taxonomy_id	266807
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2209

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2yr5A01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2yr5A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2yr5B01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2yr5B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	101.648 Å
Unit-cell length b length_b	112.624 Å
Unit-cell length c length_c	136.609 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	47.620 Å
R factor r_factor	0.1027
R_work r_work	0.1014
R_free r_free	0.1285

Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pro-enzyme of L-phenylalanine oxidase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yr5__assembly_1__model_1

2yr5__assembly_1__model_1 | I(q)

2yr5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pro-enzyme of L-phenylalanine oxidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yr5__assembly_1__model_1

2yr5__assembly_1__model_1 | I(q)

2yr5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)