SAXSdb — 2y31

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

PUTATIVE REPRESSOR SIMREG2

STREPTOMYCES ANTIBIOTICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SIMOCYCLINONE C4 × 2 PENTAETHYLENE GLYCOL × 1 TETRAETHYLENE GLYCOL × 1 CHLORIDE ION × 8 CALCIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9AMH9_STRAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 3–261 Author chain B； PDBConstruct 1–259； UniProt 3–261

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	2y31
Deposition date deposition_date	2010-12-17
Structure title title	Simocyclinone C4 bound form of TetR-like repressor SimR
Keywords keywords	TRANSCRIPTION, TETR-FAMILY; 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.

2y31__assembly_1__model_1

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

Download this curve (.dat)

2y31__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y31__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.61 Å
Rg (electron density)	23.45 Å
Total Rg	24.36 Å
Atom count	3887
Residues	474
Excluded volume	68982 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y31__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	PUTATIVE REPRESSOR SIMREG2
Molecular weight formula_weight	30240.2 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	4226

MNENEPVSIWMHPEPAGRRSARSHRTLSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSPPGRSAASERPALALEHHHHHH

Source Source

Source organism organism	STREPTOMYCES ANTIBIOTICUS
NCBI taxonomy ID ncbi_taxonomy_id	1890
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SIMOCYCLINONE C4
Molecular weight formula_weight	722.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2y31A01
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	2y31A02
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	2y31B01
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	2y31B02
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	86.570 Å
Unit-cell length b length_b	86.570 Å
Unit-cell length c length_c	349.861 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	74.970 Å
R factor r_factor	0.2002
R_work r_work	0.1978
R_free r_free	0.2461

Simocyclinone C4 bound form of TetR-like repressor SimR

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

PUTATIVE REPRESSOR SIMREG2

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

2y31__assembly_1__model_1

2y31__assembly_1__model_1 | I(q)

2y31__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Simocyclinone C4 bound form of TetR-like repressor SimR

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

PUTATIVE REPRESSOR SIMREG2

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

2y31__assembly_1__model_1

2y31__assembly_1__model_1 | I(q)

2y31__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)