SAXSdb — 1rkt

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

protein yfiR

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	UNKNOWN ATOM OR ION × 39 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O31560_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 1–205 Author chain B； PDBConstruct 1–205； UniProt 1–205

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	1rkt
Deposition date deposition_date	2003-11-23
Structure title title	Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis
Keywords keywords	;transcription regulator, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rkt__assembly_1__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	protein yfiR
Molecular weight formula_weight	23903.4 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	3548

MSPKVTKEHKDKRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYFSSTEEMFRRIIETGLDEGLRKLDKSAEHQSVWASISSYLDELTEGLRDVADTLAPVQFEYLVTAWRNEERRQYLEKRYDLFVERFSRLLQKGIDQGEFQPVQPLATIAKFFLNMNDGIIQNALYFDEEKADVSGLAESAKLYLKTVLQADEK

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	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	39

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rkta1
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.4.1.9 — Tetracyclin repressor-like, N-terminal domain

Domain ID domain_id	d1rkta2
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	d1rktb1
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.4.1.9 — Tetracyclin repressor-like, N-terminal domain

Domain ID domain_id	d1rktb2
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 (4 domains)

Domain ID domain_id	1rktA01
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	1rktA02
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	1rktB01
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	1rktB02
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	47.983 Å
Unit-cell length b length_b	48.765 Å
Unit-cell length c length_c	57.233 Å
Unit-cell angle α angle_alpha	71.96 °
Unit-cell angle β angle_beta	70.65 °
Unit-cell angle γ angle_gamma	80.20 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2105
R_work r_work	0.2081
R_free r_free	0.2542

Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis

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

protein yfiR

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis

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

protein yfiR

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)