2o3o

Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis

Method: X-RAY DIFFRACTION

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

YycI 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	CHLORIDE ION × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q45612_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–254； UniProt 31–280 Author chain B； PDBConstruct 5–254； UniProt 31–280 Author chain C； PDBConstruct 5–254； UniProt 31–280 Author chain D； PDBConstruct 5–254； UniProt 31–280 Author chain E； PDBConstruct 5–254； UniProt 31–280 Author chain F； PDBConstruct 5–254； UniProt 31–280 Author chain G； PDBConstruct 5–254； UniProt 31–280 Author chain H； PDBConstruct 5–254； UniProt 31–280 Author chain I； PDBConstruct 5–254； UniProt 31–280 Author chain J； PDBConstruct 5–254； UniProt 31–280 Author chain K； PDBConstruct 5–254； UniProt 31–280 Author chain L； PDBConstruct 5–254； UniProt 31–280

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	2o3o
Deposition date deposition_date	2006-12-01
Structure title title	Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis
Keywords keywords	two-component system, 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.

2o3o__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2o3o__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o3o__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	28.69 Å
Rg (electron density)	28.05 Å
Total Rg	28.92 Å
Atom count	3924
Residues	469
Excluded volume	70326 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o3o__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2o3o__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2o3o__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2o3o__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2o3o__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2o3o__assembly_6__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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	2o3oA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oF01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oG01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oH01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oI01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oJ01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oK01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oK02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

Domain ID domain_id	2o3oL01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	690 — YycH protein, domain 3-like

Domain ID domain_id	2o3oL02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	160 — YycH protein, domain 2

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Unit-cell length a length_a	60.792 Å
Unit-cell length b length_b	161.922 Å
Unit-cell length c length_c	180.156 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	90.000 Å
R factor r_factor	0.2140
R_work r_work	0.2120
R_free r_free	0.2620

Description description	YycI protein
Molecular weight formula_weight	29636.3 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	23401

Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis

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

YycI 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

2o3o__assembly_4__model_1

2o3o__assembly_4__model_1 | I(q)

2o3o__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

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

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis

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

YycI 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

2o3o__assembly_4__model_1

2o3o__assembly_4__model_1 | I(q)

2o3o__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)