4ac7

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

Method: X-RAY DIFFRACTION

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

UREASE SUBUNIT GAMMA

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	UREASE SUBUNIT BETA × 3 （P41021） UREASE SUBUNIT ALPHA × 3 （P41020） 1,2-ETHANEDIOL × 30 SULFATE ION × 12 NICKEL (II) ION × 6 HYDROXIDE ION × 3 CITRATE ANION × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE3_BACPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 1–100

UREASE SUBUNIT BETA

OrganismNot specified

UniProt P41021

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	UREASE SUBUNIT GAMMA × 3 （P41022） UREASE SUBUNIT ALPHA × 3 （P41020） 1,2-ETHANEDIOL × 30 SULFATE ION × 12 NICKEL (II) ION × 6 HYDROXIDE ION × 3 CITRATE ANION × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE2_BACPA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–126； UniProt 1–126

UREASE SUBUNIT ALPHA

OrganismNot specified

UniProt P41020

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	UREASE SUBUNIT GAMMA × 3 （P41022） UREASE SUBUNIT BETA × 3 （P41021） 1,2-ETHANEDIOL × 30 SULFATE ION × 12 NICKEL (II) ION × 6 HYDROXIDE ION × 3 CITRATE ANION × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE1_BACPA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–570； 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	4ac7
Deposition date deposition_date	2011-12-14
Structure title title	The crystal structure of Sporosarcina pasteurii urease in complex with citrate
Keywords keywords	HYDROLASE, BACILLUS PASTEURII; 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.

4ac7__assembly_1__model_1

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

Download this curve (.dat)

4ac7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ac7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.34 Å
Rg (electron density)	38.45 Å
Total Rg	38.81 Å
Atom count	18270
Residues	2370
Excluded volume	324120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ac7__assembly_1__model_1`	nonameric （9）	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 (9)

Entity 1 Entity 1 polymer

Description description	UREASE SUBUNIT GAMMA
Molecular weight formula_weight	11205.0 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6830

MHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS

Entity 2 Entity 2 polymer

Description description	UREASE SUBUNIT BETA
Molecular weight formula_weight	13975.5 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSNNNYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE

Entity 3 Entity 3 polymer

Description description	UREASE SUBUNIT ALPHA
Molecular weight formula_weight	61646.8 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKINRQQYAESYGPTVGDEVRLADTDLWIEVEKDYTTYGDEVNFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLKIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRLKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	HYDROXIDE ION
Molecular weight formula_weight	17.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	671

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ac7a_
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	d4ac7b_
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	d4ac7c1
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	d4ac7c2
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	4ac7A00
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	4ac7B00
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	4ac7C01
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	4ac7C02
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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7. Citations (7)

The Crystal Structure of Sporosarcina Pasteurii Urease in a Complex with Citrate Provides New Hints for Inhibitor Design.

J.Biol.Inorg.Chem. (2013)

PMID: 23412551 · DOI: 10.1007/S00775-013-0983-7 PRIMARY

Molecular Details of Urease Inhibition by Boric Acid: Insights Into the Catalytic Mechanism.

J.Am.Chem.Soc. (2004)

PMID: 15038715 · DOI: 10.1021/JA049618P

Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism.

J.Biol.Inorg.Chem. (2001)

PMID: 11713685 · DOI: 10.1007/S007750100254

The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 A Resolution.

J.Biol.Inorg.Chem. (2000)

PMID: 10766443 · DOI: 10.1007/S007750050014

;A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme from Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels. ;

Structure (1999)

PMID: 10368287 · DOI: 10.1016/S0969-2126(99)80026-4

The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65 A Resolution

J.Biol.Inorg.Chem. (1998)

DOI: 10.1007/S007750050231

;Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and Beta-Mercaptoethanol-Inhibited Urease from Bacillus Pasteurii. ;

Acta Crystallogr.,Sect.D (1998)

PMID: 9761912 · DOI: 10.1107/S0907444997013085

Unit-cell length a length_a	131.555 Å
Unit-cell length b length_b	131.555 Å
Unit-cell length c length_c	189.521 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	113.930 Å
R factor r_factor	0.1185
R_work r_work	0.1170
R_free r_free	0.1461

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

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

UREASE SUBUNIT GAMMA

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

UREASE SUBUNIT ALPHA

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

4ac7__assembly_1__model_1

4ac7__assembly_1__model_1 | I(q)

4ac7__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (7)

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

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

UREASE SUBUNIT GAMMA

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ac7__assembly_1__model_1

4ac7__assembly_1__model_1 | I(q)

4ac7__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (7)