SAXSdb — 1a5n

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

UREASE (GAMMA SUBUNIT)

Klebsiella aerogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	UREASE (BETA SUBUNIT) × 3 （P18315） UREASE (ALPHA SUBUNIT) × 3 （P18314） NICKEL (II) ION × 6 FORMIC ACID × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE3_KLEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 1–100

UREASE (BETA SUBUNIT)

Klebsiella aerogenes

UniProt P18315

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	UREASE (GAMMA SUBUNIT) × 3 （P18316） UREASE (ALPHA SUBUNIT) × 3 （P18314） NICKEL (II) ION × 6 FORMIC ACID × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE2_KLEAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–101； UniProt 1–101

UREASE (ALPHA SUBUNIT)

Klebsiella aerogenes

UniProt P18314

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	UREASE (GAMMA SUBUNIT) × 3 （P18316） UREASE (BETA SUBUNIT) × 3 （P18315） NICKEL (II) ION × 6 FORMIC ACID × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE1_KLEAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–566； UniProt 2–567

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	1a5n
Deposition date deposition_date	1998-02-17
Structure title title	K217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL
Keywords keywords	HYDROLASE (UREA AMIDO), MUTANT, NICKEL METALLOENZYME, 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.

1a5n__assembly_1__model_1

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

Download this curve (.dat)

1a5n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1a5n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.76 Å
Rg (electron density)	37.86 Å
Total Rg	38.17 Å
Atom count	17013
Residues	2256
Excluded volume	302070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1a5n__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 (6)

Entity 1 Entity 1 polymer

Description description	UREASE (GAMMA SUBUNIT)
Molecular weight formula_weight	11100.9 kDa
EC 编号 ec_number	3.5.1.5
Mutation mutation	K217A
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	5846

MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII

Source Source

Source organism organism	Klebsiella aerogenes
NCBI taxonomy ID ncbi_taxonomy_id	28451
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	UREASE (BETA SUBUNIT)
Molecular weight formula_weight	11125.7 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	B

MIPGEYHVKPGQIALNTGRATCRVVVENHGDRPIQVGSHYHFAEVNPALKFDRQQAAGYRLNIPAGTAVRFEPGQKREVELVAFAGHRAVFGFRGEVMGPL

Source Source

Source organism organism	Klebsiella aerogenes
NCBI taxonomy ID ncbi_taxonomy_id	28451
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	UREASE (ALPHA SUBUNIT)
Molecular weight formula_weight	60177.1 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	C

SNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGAATEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLAIHEDWGATPAAIDCALTVADEMDIQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF

Source Source

Source organism organism	Klebsiella aerogenes
NCBI taxonomy ID ncbi_taxonomy_id	28451
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	175

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a5na_
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	d1a5nb_
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	d1a5nc1
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	d1a5nc2
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	1a5nA00
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	1a5nB00
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	1a5nC01
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	1a5nC02
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	170.800 Å
Unit-cell length b length_b	170.800 Å
Unit-cell length c length_c	170.800 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 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1670
R_work r_work	0.1670
R_free r_free	—

K217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL

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

UREASE (GAMMA SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

UREASE (BETA SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

UREASE (ALPHA SUBUNIT)

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

1a5n__assembly_1__model_1

1a5n__assembly_1__model_1 | I(q)

1a5n__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)

K217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL

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

UREASE (GAMMA SUBUNIT)

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 (BETA SUBUNIT)

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 (ALPHA SUBUNIT)

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

1a5n__assembly_1__model_1

1a5n__assembly_1__model_1 | I(q)

1a5n__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)