SAXSdb — 4l3k

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

Urease accessory protein UreE

Sporosarcina pasteurii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 1 ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UREE_BACPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–147； UniProt 1–147 Author chain B； PDBConstruct 1–147； UniProt 1–147

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	4l3k
Deposition date deposition_date	2013-06-06
Structure title title	Crystal structure of Sporosarcina pasteurii UreE bound to Ni2+ and Zn2+
Keywords keywords	ferredoxin-like motif, urease accessory protein, metal binding, chaperone; CHAPERONE
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.

4l3k__assembly_1__model_1

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

Download this curve (.dat)

4l3k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4l3k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.28 Å
Rg (electron density)	27.21 Å
Total Rg	27.59 Å
Atom count	2294
Residues	282
Excluded volume	41039 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4l3k__assembly_1__model_1`	dimeric （2）	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 accessory protein UreE
Molecular weight formula_weight	17428.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2460

MLITKIVGHIDDYESSDKKVDWLEVEWEDLNKRILRKETENGTDIAIKLENSGTLRYGDVLYESDDTLIAIRTKLEKVYVIKPQTMQEMGKMAFEIGNRHTMCIIEDDEILVRYDKTLEKLIDEVGVSYEQSERRFKEPFKYRGHQH

Source Source

Source organism organism	Sporosarcina pasteurii
NCBI taxonomy ID ncbi_taxonomy_id	1474
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4l3ka1
Class class	b — All beta proteins
Fold Fold fold	b.107 — Urease metallochaperone UreE, N-terminal domain
Superfamily Superfamily superfamily	b.107.1 — Urease metallochaperone UreE, N-terminal domain
Family Family family	b.107.1.1 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	d4l3ka2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.38 — Urease metallochaperone UreE, C-terminal domain
Family Family family	d.58.38.1 — Urease metallochaperone UreE, C-terminal domain

Domain ID domain_id	d4l3kb1
Class class	b — All beta proteins
Fold Fold fold	b.107 — Urease metallochaperone UreE, N-terminal domain
Superfamily Superfamily superfamily	b.107.1 — Urease metallochaperone UreE, N-terminal domain
Family Family family	b.107.1.1 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	d4l3kb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.38 — Urease metallochaperone UreE, C-terminal domain
Family Family family	d.58.38.1 — Urease metallochaperone UreE, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	4l3kA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	4l3kA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	790 — UreE, C-terminal domain

Domain ID domain_id	4l3kB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	4l3kB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	790 — UreE, C-terminal domain

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Unit-cell length a length_a	91.329 Å
Unit-cell length b length_b	91.329 Å
Unit-cell length c length_c	82.792 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
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	45.660 Å
R factor r_factor	0.1726
R_work r_work	0.1708
R_free r_free	0.2070

Crystal structure of Sporosarcina pasteurii UreE bound to Ni2+ and Zn2+

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

Urease accessory protein UreE

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

4l3k__assembly_1__model_1

4l3k__assembly_1__model_1 | I(q)

4l3k__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 non-polymer

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 Sporosarcina pasteurii UreE bound to Ni2+ and Zn2+

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

Urease accessory protein UreE

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

4l3k__assembly_1__model_1

4l3k__assembly_1__model_1 | I(q)

4l3k__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 non-polymer

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)