SAXSdb — 1yoe

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

Hypothetical protein ybeK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	alpha-D-ribofuranose × 4 CALCIUM ION × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	alpha-D-ribofuranose × 2 CALCIUM ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	alpha-D-ribofuranose × 2 CALCIUM ION × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	alpha-D-ribofuranose × 4 CALCIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBEK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–322； UniProt 2–311

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	1yoe
Deposition date deposition_date	2005-01-27
Structure title title	Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
Keywords keywords	Pyrimidine nucleoside hydrolase, bacterial nucleosidase, ribose, enzyme-product complex, 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.

1yoe__assembly_1__model_1

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

Download this curve (.dat)

1yoe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yoe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.65 Å
Rg (electron density)	33.96 Å
Total Rg	34.30 Å
Atom count	9224
Residues	1208
Excluded volume	166000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yoe__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yoe__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yoe__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yoe__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein ybeK
Molecular weight formula_weight	35128.1 kDa
EC 编号 ec_number	3.2.2.8
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	2565

MRGSHHHHHHGSALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	alpha-D-ribofuranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	215

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1yoea1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.70 — Nucleoside hydrolase
Superfamily Superfamily superfamily	c.70.1 — Nucleoside hydrolase
Family Family family	c.70.1.0 — automated matches

Domain ID domain_id	d1yoea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1yoeA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	245 — Inosine-uridine Nucleoside N-ribohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonucleoside hydrolase-like

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Unit-cell length a length_a	76.466 Å
Unit-cell length b length_b	84.062 Å
Unit-cell length c length_c	112.483 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1681
R_work r_work	0.1673
R_free r_free	0.1928

Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

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

Hypothetical protein ybeK

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

1yoe__assembly_1__model_1

1yoe__assembly_1__model_1 | I(q)

1yoe__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (4)

Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

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

Hypothetical protein ybeK

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

1yoe__assembly_1__model_1

1yoe__assembly_1__model_1 | I(q)

1yoe__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (4)