3whc

Crystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA

Method: X-RAY DIFFRACTION

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

Fatty acid metabolism regulator 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	STEAROYL-COENZYME A × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	STEAROYL-COENZYME A × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	STEAROYL-COENZYME A × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FADR_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 1–194 Author chain B； PDBConstruct 1–194； UniProt 1–194 Author chain C； PDBConstruct 1–194； UniProt 1–194 Author chain D； PDBConstruct 1–194； UniProt 1–194 Author chain E； PDBConstruct 1–194； UniProt 1–194 Author chain F； PDBConstruct 1–194； UniProt 1–194

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	3whc
Deposition date deposition_date	2013-08-23
Structure title title	Crystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA
Keywords keywords	transcriptional regulator, fatty acid degradation, TRANSCRIPTION; TRANSCRIPTION
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.

3whc__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3whc__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3whc__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.39 Å
Rg (electron density)	21.30 Å
Total Rg	22.17 Å
Atom count	3054
Residues	378
Excluded volume	55184 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3whc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3whc__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3whc__assembly_3__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	Fatty acid metabolism regulator protein
Molecular weight formula_weight	22007.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9291

MKQKRPKYMQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKMGQFIERMEEDIKEKATAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQSGEIKEGLDVRLARQMIFGTIDETVTTWVMNDQKYDLVALSNSVLELLVSGIHNK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	STEAROYL-COENZYME A
Molecular weight formula_weight	1034.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3whca1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.0 — automated matches

Domain ID domain_id	d3whca2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d3whcb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.0 — automated matches

Domain ID domain_id	d3whcb2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d3whcc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.0 — automated matches

Domain ID domain_id	d3whcc2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d3whcd1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.0 — automated matches

Domain ID domain_id	d3whcd2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d3whce1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.0 — automated matches

Domain ID domain_id	d3whce2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d3whcf1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.0 — automated matches

Domain ID domain_id	d3whcf2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	3whcA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3whcA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	3whcB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3whcB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	3whcC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3whcC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	3whcD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3whcD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	3whcE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3whcE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	3whcF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3whcF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

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Unit-cell length a length_a	70.305 Å
Unit-cell length b length_b	88.762 Å
Unit-cell length c length_c	199.952 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2403
R_work r_work	0.2386
R_free r_free	0.2711

Crystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA

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

Fatty acid metabolism regulator 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

3whc__assembly_2__model_1

3whc__assembly_2__model_1 | I(q)

3whc__assembly_2__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA

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

Fatty acid metabolism regulator 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

3whc__assembly_2__model_1

3whc__assembly_2__model_1 | I(q)

3whc__assembly_2__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)