SAXSdb — 2bas

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

YkuI protein

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	BETA-MERCAPTOETHANOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O35014_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–431； UniProt 1–407 Author chain B； PDBConstruct 25–431； UniProt 1–407

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	2bas
Deposition date deposition_date	2005-10-14
Structure title title	Crystal Structure of the Bacillus subtilis YkuI Protein, with an EAL Domain.
Keywords keywords	;YkuI protein, EAL domain, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, SIGNALING PROTEIN ;; SIGNALING PROTEIN
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.

2bas__assembly_1__model_1

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

Download this curve (.dat)

2bas__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bas__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.90 Å
Rg (electron density)	29.90 Å
Total Rg	30.66 Å
Atom count	6660
Residues	780
Excluded volume	118960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bas__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 (3)

Entity 1 Entity 1 polymer

Description description	YkuI protein
Molecular weight formula_weight	51266.9 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	6915

MHHHHHHSSGVDLGTENLYFQSNAMLDPLDILTNIDDVLPYYQAIFSAEEQKVVGYEVLGRILADSEIQSLGPFFLDAGIPEEYKLEVDNRIIRQALDRFLEADSDLLIFMNQDANLLMLDHGESFLELLKEYEAKGIELHRFVLEITEHNFEGDIEQLYHMLAYYRTYGIKIAVDNIGKESSNLDRIALLSPDLLKIDLQALKVSQPSPSYEHVLYSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYLVSPSETFLERDVLKQRLKTEFHQFITHEKKKLETVYEHSEQFYKRVHQAVTSLRKNNLSSDDDFIKKLAEELTDCSFRIYMCDEEGDQLTGNVFKQDGEWIYQPEYAEKNWSWRPYFLENIMRMRNLRKGFFSDLYSDLETGEMIRTFSYPMDDQMYLFIDLPYSYLYEQDGLI

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	255

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2basa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.33 — EAL domain-like
Family Family family	c.1.33.1 — EAL domain

Domain ID domain_id	d2basa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.2 — YkuI C-terminal domain-like

Domain ID domain_id	d2basb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.33 — EAL domain-like
Family Family family	c.1.33.1 — EAL domain

Domain ID domain_id	d2basb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.2 — YkuI C-terminal domain-like

Domain ID domain_id	d2basb3
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 (6 domains)

Domain ID domain_id	2basA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	2basA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	2basA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	2basB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	450 — EAL domain

Domain ID domain_id	2basB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	2basB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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Unit-cell length a length_a	46.335 Å
Unit-cell length b length_b	125.271 Å
Unit-cell length c length_c	167.962 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	24.040 Å
R factor r_factor	0.2068
R_work r_work	0.2026
R_free r_free	0.2870

Crystal Structure of the Bacillus subtilis YkuI Protein, with an EAL Domain.

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

YkuI protein

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

2bas__assembly_1__model_1

2bas__assembly_1__model_1 | I(q)

2bas__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of the Bacillus subtilis YkuI Protein, with an EAL Domain.

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

YkuI protein

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

2bas__assembly_1__model_1

2bas__assembly_1__model_1 | I(q)

2bas__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

7. Citations (1)