SAXSdb — 3dqy

▼

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

Toluene 1,2-dioxygenase system ferredoxin subunit

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE2/S2 (INORGANIC) CLUSTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TODB_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–106； UniProt 2–107

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dqy
Deposition date deposition_date	2008-07-10
Structure title title	Crystal structure of Toluene 2,3-Dioxygenase Ferredoxin
Keywords keywords	;Rieske, iron-sulfur cluster, 2Fe-2S, Aromatic hydrocarbons catabolism, Electron transport, Iron, Iron-sulfur, Metal-binding, Transport, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3dqy__assembly_1__model_1

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

Download this curve (.dat)

3dqy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dqy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.22 Å
Rg (electron density)	12.99 Å
Total Rg	14.17 Å
Atom count	830
Residues	105
Excluded volume	14779 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dqy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Toluene 1,2-dioxygenase system ferredoxin subunit
Molecular weight formula_weight	11787.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	906

TWTYILRQGDLPPGEMQRYEGGPEPVMVCNVDGEFFAVQDTCTHGDWALSDGYLDGDIVECTLHFGKFCVRTGKVKALPACKPIKVFPIKVEGDEVHVDLDNGELK

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3dqya_
Class class	b — All beta proteins
Fold Fold fold	b.33 — ISP domain
Superfamily Superfamily superfamily	b.33.1 — ISP domain
Family Family family	b.33.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3dqyA00
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

▶

Unit-cell length a length_a	30.544 Å
Unit-cell length b length_b	52.090 Å
Unit-cell length c length_c	30.948 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	28.398 Å
R factor r_factor	0.1841
R_work r_work	0.1835
R_free r_free	0.1949

Crystal structure of Toluene 2,3-Dioxygenase Ferredoxin

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

Toluene 1,2-dioxygenase system ferredoxin subunit

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

3dqy__assembly_1__model_1

3dqy__assembly_1__model_1 | I(q)

3dqy__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Toluene 2,3-Dioxygenase Ferredoxin

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

Toluene 1,2-dioxygenase system ferredoxin subunit

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

3dqy__assembly_1__model_1

3dqy__assembly_1__model_1 | I(q)

3dqy__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)