SAXSdb — 1e9z

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

UREASE SUBUNIT ALPHA

HELICOBACTER PYLORI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	UREASE SUBUNIT BETA × 12 （P69996） NICKEL (II) ION × 24 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE23_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–238； UniProt 1–238

UREASE SUBUNIT BETA

HELICOBACTER PYLORI

UniProt P69996

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	UREASE SUBUNIT ALPHA × 12 （P14916） NICKEL (II) ION × 24 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE1_HELPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–569； UniProt 1–569

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	1e9z
Deposition date deposition_date	2000-11-01
Structure title title	Crystal structure of Helicobacter pylori urease
Keywords keywords	HYDROLASE; HYDROLASE
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.

1e9z__assembly_1__model_1

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

Download this curve (.dat)

1e9z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1e9z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.66 Å
Rg (electron density)	59.82 Å
Total Rg	60.10 Å
Atom count	74400
Residues	9672
Excluded volume	1321200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1e9z__assembly_1__model_1`	24-meric （24）	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 (4)

Entity 1 Entity 1 polymer

Description description	UREASE SUBUNIT ALPHA
Molecular weight formula_weight	26571.7 kDa
EC 编号 ec_number	3.5.1.5
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	6278

MKLTPKELDKLMLHYAGELAKKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHEVGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLDIAAGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGAKSDDNYVKTIKE

Source Source

Source organism organism	HELICOBACTER PYLORI
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	UREASE SUBUNIT BETA
Molecular weight formula_weight	61745.4 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTGIYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGGTGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNASNDASLADQIEAGAIGFKIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMDMLMVCHHLDKSIKEDVQFADSRIRPQTIAAEDTLHDMGAFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGDNDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYREMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNVTKKDMQFNNTTAHIEVNPETYHVFVDGKEVTSKPANKVSLAQLFSIF

Source Source

Source organism organism	HELICOBACTER PYLORI
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1e9za1
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.3 — Urease, beta-subunit
Family Family family	b.85.3.1 — Urease, beta-subunit

Domain ID domain_id	d1e9za2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.8 — Urease, gamma-subunit
Superfamily Superfamily superfamily	d.8.1 — Urease, gamma-subunit
Family Family family	d.8.1.1 — Urease, gamma-subunit

Domain ID domain_id	d1e9zb1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.1 — alpha-Subunit of urease

Domain ID domain_id	d1e9zb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.2 — alpha-subunit of urease, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1e9zA01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	150 — Urease, subunit B
Homologous superfamily homologous superfamily	10 — Urease, beta subunit

Domain ID domain_id	1e9zA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	280 — Urease; subunit A
Homologous superfamily homologous superfamily	10 — Urease, gamma-like subunit

Domain ID domain_id	1e9zB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1e9zB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	177.910 Å
Unit-cell length b length_b	177.910 Å
Unit-cell length c length_c	177.910 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2840

Crystal structure of Helicobacter pylori urease

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

UREASE SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

UREASE SUBUNIT BETA

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

1e9z__assembly_1__model_1

1e9z__assembly_1__model_1 | I(q)

1e9z__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Helicobacter pylori urease

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

UREASE SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UREASE SUBUNIT BETA

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

1e9z__assembly_1__model_1

1e9z__assembly_1__model_1 | I(q)

1e9z__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)