SAXSdb — 2q0o

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

Probable transcriptional activator protein traR

Rhizobium sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Probable transcriptional repressor traM × 2 （P55408） 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAR_RHISN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–236； UniProt 1–236 Author chain B； PDBConstruct 1–236； UniProt 1–236

Probable transcriptional repressor traM

Rhizobium sp.

UniProt P55408

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Probable transcriptional activator protein traR × 2 （P55407） 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAM_RHISN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–107； UniProt 1–107 Author chain D； PDBConstruct 1–107； UniProt 1–107

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	2q0o
Deposition date deposition_date	2007-05-22
Structure title title	Crystal structure of an anti-activation complex in bacterial quorum sensing
Keywords keywords	helix-turn-helix, two-helix coiled coil, 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.

2q0o__assembly_1__model_1

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

Download this curve (.dat)

2q0o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2q0o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.75 Å
Rg (electron density)	31.23 Å
Total Rg	31.68 Å
Atom count	5084
Residues	643
Excluded volume	90617 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q0o__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Probable transcriptional activator protein traR
Molecular weight formula_weight	26324.5 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	5568

MSVNGNLRSLIDMLEAAQDGHMIKIALRSFAHSCGYDRFAYLQKDGTQVRTFHSYPGPWESIYLGSDYFNIDPVLAEAKRRRDVFFWTADAWPARGSSPLRRFRDEAISHGIRCGVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIAAKTVLNPKQMLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRGLV

Source Source

Source organism organism	Rhizobium sp.
NCBI taxonomy ID ncbi_taxonomy_id	394
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Probable transcriptional repressor traM
Molecular weight formula_weight	12215.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MNDMGSSEVNDENKEKEARYSVMTKSELEALAVSAIREHRRLLWADQAVYEEWLRASDDPSISGPVLQTLQDEYVARQKRSEAQQEELSDILDALGFVPDVPFDDDN

Source Source

Source organism organism	Rhizobium sp.
NCBI taxonomy ID ncbi_taxonomy_id	394
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
Molecular weight formula_weight	241.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	484

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2q0oA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	2q0oA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2q0oB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	2q0oB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2q0oC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	160 — HR1 repeat

Domain ID domain_id	2q0oD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	160 — HR1 repeat

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Unit-cell length a length_a	56.900 Å
Unit-cell length b length_b	62.480 Å
Unit-cell length c length_c	65.500 Å
Unit-cell angle α angle_alpha	94.87 °
Unit-cell angle β angle_beta	110.45 °
Unit-cell angle γ angle_gamma	99.17 °
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	2.000 Å
Low-resolution limit resolution_low	39.850 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2760

Crystal structure of an anti-activation complex in bacterial quorum sensing

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

Probable transcriptional activator protein traR

State in the Current Structure

Other States of the Same Protein in the Database

Probable transcriptional repressor traM

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

2q0o__assembly_1__model_1

2q0o__assembly_1__model_1 | I(q)

2q0o__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of an anti-activation complex in bacterial quorum sensing

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

Probable transcriptional activator protein traR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Probable transcriptional repressor traM

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

2q0o__assembly_1__model_1

2q0o__assembly_1__model_1 | I(q)

2q0o__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)