SAXSdb — 2h4o

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

YonK protein

Bacillus subtilis

UniProt O31947

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O31947_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–63； UniProt 1–63 Author chain B； PDBConstruct 1–63； UniProt 1–63 Author chain C； PDBConstruct 1–63； UniProt 1–63 Author chain D； PDBConstruct 1–63； UniProt 1–63

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	2h4o
Deposition date deposition_date	2006-05-24
Structure title title	X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415
Keywords keywords	;PSI, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, Bsu2107 (YonK protein), STRUCTURAL GENOMICS, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2h4o__assembly_1__model_1

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

Download this curve (.dat)

2h4o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2h4o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.48 Å
Rg (electron density)	26.08 Å
Total Rg	27.12 Å
Atom count	4008
Residues	480
Excluded volume	71757 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2h4o__assembly_1__model_1`	octameric （8）	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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2h4oa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.368 — YonK-like
Superfamily Superfamily superfamily	d.368.1 — YonK-like
Family Family family	d.368.1.1 — Yonk-like

Domain ID domain_id	d2h4ob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.368 — YonK-like
Superfamily Superfamily superfamily	d.368.1 — YonK-like
Family Family family	d.368.1.1 — Yonk-like

Domain ID domain_id	d2h4oc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.368 — YonK-like
Superfamily Superfamily superfamily	d.368.1 — YonK-like
Family Family family	d.368.1.1 — Yonk-like

Domain ID domain_id	d2h4od_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.368 — YonK-like
Superfamily Superfamily superfamily	d.368.1 — YonK-like
Family Family family	d.368.1.1 — Yonk-like

CATH v4.4 (4 domains)

Domain ID domain_id	2h4oA00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2h4oB00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2h4oC00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2h4oD00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	101.016 Å
Unit-cell length b length_b	72.201 Å
Unit-cell length c length_c	48.935 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	28.340 Å
R factor r_factor	0.2630
R_work r_work	0.2630
R_free r_free	0.3010

Description description	YonK protein
Molecular weight formula_weight	9012.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2032

X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415

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

YonK 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

2h4o__assembly_1__model_1

2h4o__assembly_1__model_1 | I(q)

2h4o__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415

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

YonK 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

2h4o__assembly_1__model_1

2h4o__assembly_1__model_1 | I(q)

2h4o__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)