SAXSdb — 5y2p

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

Uric acid degradation bifunctional protein

Bacillus sp. (strain TB-90)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	8-AZAXANTHINE × 4 OXYGEN MOLECULE × 4 SULFATE ION × 2 1,2-ETHANEDIOL × 12 POTASSIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUCL_BACSB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 178–489 Author chain B； PDBConstruct 1–312； UniProt 178–489

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	5y2p
Deposition date deposition_date	2017-07-26
Structure title title	Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% RH
Keywords keywords	Protein engineering, Oxidase, pH dependence, enzyme activation, flexibility, loop plasticity, 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.

5y2p__assembly_1__model_1

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

Download this curve (.dat)

5y2p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5y2p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.95 Å
Rg (electron density)	30.54 Å
Total Rg	31.45 Å
Atom count	19246
Residues	1210
Excluded volume	173760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5y2p__assembly_1__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Uric acid degradation bifunctional protein
Molecular weight formula_weight	35714.1 kDa
EC 编号 ec_number	1.7.3.3
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	10577

VMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQEDLPHENIL

Source Source

Source organism organism	Bacillus sp. (strain TB-90)
NCBI taxonomy ID ncbi_taxonomy_id	36824
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	8-AZAXANTHINE
Molecular weight formula_weight	153.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	680

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5y2pa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d5y2pa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d5y2pb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d5y2pb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

CATH v4.4 (2 domains)

Domain ID domain_id	5y2pA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	5y2pB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

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Unit-cell length a length_a	71.095 Å
Unit-cell length b length_b	133.885 Å
Unit-cell length c length_c	145.797 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	40.121 Å
R factor r_factor	0.1584
R_work r_work	0.1574
R_free r_free	0.1769

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% RH

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

Uric acid degradation bifunctional protein

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

5y2p__assembly_1__model_1

5y2p__assembly_1__model_1 | I(q)

5y2p__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (3)

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% RH

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

Uric acid degradation bifunctional protein

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

5y2p__assembly_1__model_1

5y2p__assembly_1__model_1 | I(q)

5y2p__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (3)