SAXSdb — 4fib

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

Uncharacterized protein ydhK

Bacillus subtilis subsp. subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YDHK_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–121； UniProt 83–202 Author chain B； PDBConstruct 2–121； UniProt 83–202 Author chain C； PDBConstruct 2–121； UniProt 83–202

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	4fib
Deposition date deposition_date	2012-06-08
Structure title title	Crystal structure of the ydhK protein from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR518A.
Keywords keywords	Structural Genomics, PSI-Biology, Northeast Structural Genomics Consortium, NESG, SR518A, ydhK, DUF1541, PF07563, 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.

4fib__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4fib__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4fib__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	15.29 Å
Rg (electron density)	14.30 Å
Total Rg	15.28 Å
Atom count	947
Residues	118
Excluded volume	16816 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4fib__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4fib__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4fib__assembly_3__model_1`	monomeric （1）	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) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4fibA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1130 —

Domain ID domain_id	4fibA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	4fibB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1130 —

Domain ID domain_id	4fibB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	4fibC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1130 —

Domain ID domain_id	4fibC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	520 —

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Unit-cell length a length_a	50.861 Å
Unit-cell length b length_b	69.493 Å
Unit-cell length c length_c	61.487 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.997 Å
Low-resolution limit resolution_low	46.486 Å
R factor r_factor	0.2060
R_work r_work	0.2040
R_free r_free	0.2550

Description description	Uncharacterized protein ydhK
Molecular weight formula_weight	14605.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2997

Crystal structure of the ydhK protein from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR518A.

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

Uncharacterized protein ydhK

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

4fib__assembly_3__model_1

4fib__assembly_3__model_1 | I(q)

4fib__assembly_3__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Bacillus subtilis subsp. subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
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	151

Crystal structure of the ydhK protein from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR518A.

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

Uncharacterized protein ydhK

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

4fib__assembly_3__model_1

4fib__assembly_3__model_1 | I(q)

4fib__assembly_3__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)