2yzb

Crystal structure of uricase from Arthrobacter globiformis in complex with uric acid (substrate)

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	4 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	4 / 0 / 0 / 0	Consistent with protein count

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	2yzb
Deposition date deposition_date	2007-05-05
Structure title title	Crystal structure of uricase from Arthrobacter globiformis in complex with uric acid (substrate)
Keywords keywords	uricase, oxidoreductase, uric acid; 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.

2yzb__assembly_1__model_1

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

Download this curve (.dat)

2yzb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yzb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.28 Å
Rg (electron density)	29.85 Å
Total Rg	30.64 Å
Atom count	9190
Residues	1148
Excluded volume	160540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yzb__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yzb__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Uricase
Molecular weight formula_weight	33900.6 kDa
EC 编号 ec_number	1.7.3.3
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	19734

MTATAETSTGTKVVLGQNQYGKAEVRLVKVTRNTARHEIQDLNVTSQLRGDFEAAHTAGDNAHVVATDTQKNTVYAFARDGFATTEEFLLRLGKHFTEGFDWVTGGRWAAQQFFWDRINDHDHAFSRNKSEVRTAVLEISGSEQAIVAGIEGLTVLKSTGSEFHGFPRDKYTTLQETTDRILATDVSARWRYNTVEVDFDAVYASVRGLLLKAFAETHSLALQQTMYEMGRAVIETHPEIDEIKMSLPNKHHFLVDLQPFGQDNPNEVFYAADRPYGLIEATIQREGSRADHPIWSNIAGFC

Entity 2 Entity 2 non-polymer

Description description	URIC ACID
Molecular weight formula_weight	168.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1361

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2yzba1
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	d2yzba2
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	d2yzbb1
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	d2yzbb2
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	d2yzbc1
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	d2yzbc2
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	d2yzbd1
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	d2yzbd2
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	d2yzbe1
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	d2yzbe2
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	d2yzbf1
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	d2yzbf2
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	d2yzbg1
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	d2yzbg2
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	d2yzbh1
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	d2yzbh2
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 (8 domains)

Domain ID domain_id	2yzbA00
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	2yzbB00
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	2yzbC00
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	2yzbD00
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	2yzbE00
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	2yzbF00
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	2yzbG00
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	2yzbH00
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	84.480 Å
Unit-cell length b length_b	123.240 Å
Unit-cell length c length_c	284.550 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	32

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	0.2226