SAXSdb — 7q04

▼

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

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1

Comamonas sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 × 3 （Q3C1D5） Lysozyme × 1 （P00698） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPDB1_COMSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–154； UniProt 1–154 Author chain B； PDBConstruct 1–154； UniProt 1–154 Author chain C； PDBConstruct 1–154； UniProt 1–154

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2

Comamonas sp.

UniProt Q3C1D5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 × 3 （Q3C1E2） Lysozyme × 1 （P00698） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPDA2_COMSP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 3–415； UniProt 1–413 Author chain E； PDBConstruct 3–415； UniProt 1–413 Author chain F； PDBConstruct 3–415； UniProt 1–413

Lysozyme

OrganismNot specified

UniProt P00698

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 × 3 （Q3C1E2） Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 × 3 （Q3C1D5） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYSC_CHICK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–129； UniProt 19–147

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	7q04
Deposition date deposition_date	2021-10-14
Structure title title	Crystal structure of TPADO in a substrate-free state
Keywords keywords	terephthalic acid, TPA, 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.

7q04__assembly_1__model_1

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

Download this curve (.dat)

7q04__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7q04__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.93 Å
Rg (electron density)	35.81 Å
Total Rg	36.39 Å
Atom count	26897
Residues	1741
Excluded volume	240740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7q04__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
Molecular weight formula_weight	17249.4 kDa
EC 编号 ec_number	1.14.12.15
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	27325

MINEIQIAAFNAAYAKTVDSDAMEQWPTFFTKDCHYRVTNVDNHAEGLAAGIVWADSQDMLTDRISALREANIYERHRYRHILGLPSIQSGDATQASASTPFMVLRIMHTGETEVFASGEYLDKFTTIDGKLRLQERIAVCDSTVTDTLMALPL

Source Source

Source organism organism	Comamonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	34028
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
Molecular weight formula_weight	48166.8 kDa
EC 编号 ec_number	1.14.12.15
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MGMQESIIQWHGATNTRVPFGIYTDTANADQEQQRIYRGEVWNYLCLESEIPGAGDFRTTFAGETPIVVVRDADQEIYAFENRCAHRGALIALEKSGRTDSFQCVYHAWSYNRQGDLTGVAFEKGVKGQGGMPASFCKEEHGPRKLRVAVFCGLVFGSFSEDVPSIEDYLGPEICERIERVLHKPVEVIGRFTQKLPNNWKLYFENVKDSYHASLLHMFFTTFELNRLSQKGGVIVDESGGHHVSYSMIDRGAKDDSYKDQAIRSDNERYRLKDPSLLEGFEEFEDGVTLQILSVFPGFVLQQIQNSIAVRQLLPKSISSSELNWTYLGYADDSAEQRKVRLKQANLIGPAGFISMEDGAVGGFVQRGIAGAANLDAVIEMGGDHEGSSEGRATETSVRGFWKAYRKHMGQEMQAENLYFQGHHHHHH

Source Source

Source organism organism	Comamonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	34028
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Lysozyme
Molecular weight formula_weight	14331.2 kDa
EC 编号 ec_number	3.2.1.17
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

Entity 4 Entity 4 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	408

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7q04D01
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

Domain ID domain_id	7q04E01
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

Domain ID domain_id	7q04F01
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

Domain ID domain_id	7q04H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	220.807 Å
Unit-cell length b length_b	220.807 Å
Unit-cell length c length_c	84.093 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	18

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.281 Å
Low-resolution limit resolution_low	191.224 Å
R factor r_factor	—
R_work r_work	0.1788
R_free r_free	0.2249

Crystal structure of TPADO in a substrate-free state

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

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1

State in the Current Structure

Other States of the Same Protein in the Database

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2

State in the Current Structure

Other States of the Same Protein in the Database

Lysozyme

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

7q04__assembly_1__model_1

7q04__assembly_1__model_1 | I(q)

7q04__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of TPADO in a substrate-free state

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

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lysozyme

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

7q04__assembly_1__model_1

7q04__assembly_1__model_1 | I(q)

7q04__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)