SAXSdb — 5frc

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

URICASE

ASPERGILLUS FLAVUS

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 SODIUM ION × 4 OXYGEN MOLECULE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URIC_ASPFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–302； UniProt 2–302

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	5frc
Deposition date deposition_date	2015-12-16
Structure title title	Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure
Keywords keywords	OXIDOREDUCTASE, URATE OXIDASE, DIOXYGEN, PRESSURE, FLASH FREEZING; 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.

5frc__assembly_1__model_1

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

Download this curve (.dat)

5frc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5frc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.70 Å
Rg (electron density)	30.55 Å
Total Rg	31.36 Å
Atom count	9504
Residues	1180
Excluded volume	168100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5frc__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 (5)

Entity 1 Entity 1 polymer

Description description	URICASE
Molecular weight formula_weight	34183.6 kDa
EC 编号 ec_number	1.7.3.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2841

XSAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRSSLKSKL

Source Source

Source organism organism	ASPERGILLUS FLAVUS
NCBI taxonomy ID ncbi_taxonomy_id	5059
Host organism host_organism	SACCHAROMYCES CEREVISIAE

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	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	370

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5frca1
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	d5frca2
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 (1 domains)

Domain ID domain_id	5frcA00
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	80.898 Å
Unit-cell length b length_b	95.351 Å
Unit-cell length c length_c	104.672 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.443 Å
Low-resolution limit resolution_low	47.675 Å
R factor r_factor	0.1427
R_work r_work	0.1415
R_free r_free	0.1648

Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure

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

URICASE

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

5frc__assembly_1__model_1

5frc__assembly_1__model_1 | I(q)

5frc__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure

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

URICASE

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

5frc__assembly_1__model_1

5frc__assembly_1__model_1 | I(q)

5frc__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)