3q3o

Toluene 4 monooxygenase HD complex with phenol

Method: X-RAY DIFFRACTION

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

Toluene-4-monooxygenase system protein A

Pseudomonas mendocina

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Toluene-4-monooxygenase system protein E × 2 （Q00460） Toluene-4-monooxygenase system protein B × 2 （Q00457） Toluene-4-monooxygenase system protein D × 2 （Q00459） FE (III) ION × 4 PHENOL × 12 PENTAETHYLENE GLYCOL × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6Q8Q7_PSEME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–500； UniProt 1–500

Toluene-4-monooxygenase system protein E

Pseudomonas mendocina

UniProt Q00460

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Toluene-4-monooxygenase system protein A × 2 （Q6Q8Q7） Toluene-4-monooxygenase system protein B × 2 （Q00457） Toluene-4-monooxygenase system protein D × 2 （Q00459） FE (III) ION × 4 PHENOL × 12 PENTAETHYLENE GLYCOL × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TMOE_PSEME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–307； UniProt 1–307

Toluene-4-monooxygenase system protein B

Pseudomonas mendocina

UniProt Q00457

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Toluene-4-monooxygenase system protein A × 2 （Q6Q8Q7） Toluene-4-monooxygenase system protein E × 2 （Q00460） Toluene-4-monooxygenase system protein D × 2 （Q00459） FE (III) ION × 4 PHENOL × 12 PENTAETHYLENE GLYCOL × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TMOB_PSEME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–84； UniProt 1–84

Toluene-4-monooxygenase system protein D

Pseudomonas mendocina

UniProt Q00459

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Toluene-4-monooxygenase system protein A × 2 （Q6Q8Q7） Toluene-4-monooxygenase system protein E × 2 （Q00460） Toluene-4-monooxygenase system protein B × 2 （Q00457） FE (III) ION × 4 PHENOL × 12 PENTAETHYLENE GLYCOL × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TMOD_PSEME
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–103； UniProt 1–103

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	3q3o
Deposition date deposition_date	2010-12-22
Structure title title	Toluene 4 monooxygenase HD complex with phenol
Keywords keywords	aromatic hydrocarbon catabolism, iron, multi-component monooxygenase, aromatic hydroxylation, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

3q3o__assembly_1__model_1

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

Download this curve (.dat)

3q3o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3q3o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.76 Å
Rg (electron density)	39.23 Å
Total Rg	39.64 Å
Atom count	16164
Residues	1960
Excluded volume	285220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3q3o__assembly_1__model_1`	octameric （8）	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 (8)

Entity 1 Entity 1 polymer

Description description	Toluene-4-monooxygenase system protein A
Molecular weight formula_weight	58169.3 kDa
EC 编号 ec_number	1.14.13.-
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	8784

MAMHPRKDWYELTRATNWTPSYVTEEQLFPERMSGHMGIPLEKWESYDEPYKTSYPEYVSIQREKDAGAYSVKAALERAKIYENSDPGWISTLKSHYGAIAVGEYAAVTGEGRMARFSKAPGNRNMATFGMMDELRHGQLQLFFPHEYCKKDRQFDWAWRAYHSNEWAAIAAKHFFDDIITGRDAISVAIMLTFSFETGFTNMQFLGLAADAAEAGDYTFANLISSIQTDESRHAQQGGPALQLLIENGKREEAQKKVDMAIWRAWRLFAVLTGPVMDYYTPLEDRSQSFKEFMYEWIIGQFERSLIDLGLDKPWYWDLFLKDIDELHHSYHMGVWYWRTTAWWNPAAGVTPEERDWLEEKYPGWNKRWGRCWDVITENVLNDRMDLVSPETLPSVCNMSQIPLVGVPGDDWNIEVFSLEHNGRLYHFGSEVDRWVFQQDPVQYQNHMNIVDRFLAGQIQPMTLEGALKYMGFQSIEEMGKDAHDFAWADKCKPAMKKSA

Source Source

Source organism organism	Pseudomonas mendocina
NCBI taxonomy ID ncbi_taxonomy_id	300
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Toluene-4-monooxygenase system protein E
Molecular weight formula_weight	36176.6 kDa
EC 编号 ec_number	1.14.13.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSFESKKPMRTWSHLAEMRKKPSEYDIVSRKLHYSTNNPDSPWELSPDSPMNLWYKQYRNASPLKHDNWDAFTDPDQLVYRTYNLMQDGQESYVQSLFDQFNEREHDQMVREGWEHTMARCYSPLRYLFHCLQMSSAYVQQMAPASTISNCCILQTADSLRWLTHTAYRTHELSLTYPDAGLGEHERELWEKEPGWQGLRELMEKQLTAFDWGEAFVSLNLVVKPMIVESIFKPLQQQAWENNDTLLPLLIDSQLKDAERHSRWSKALVKHALENPDNHAVIEGWIEKWRPLADRAAEAYLSMLSSD

Source Source

Source organism organism	Pseudomonas mendocina
NCBI taxonomy ID ncbi_taxonomy_id	300
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Toluene-4-monooxygenase system protein B
Molecular weight formula_weight	9601.0 kDa
EC 编号 ec_number	1.14.13.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSAFPVHAAFEKDFLVQLVVVDLNDSMDQVAEKVAYHCVNRRVAPREGVMRVRKHRSTELFPRDMTIAESGLNPTEVIDVVFEE

Source Source

Source organism organism	Pseudomonas mendocina
NCBI taxonomy ID ncbi_taxonomy_id	300
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Toluene-4-monooxygenase system protein D
Molecular weight formula_weight	11629.0 kDa
EC 编号 ec_number	1.14.13.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSTLADQALHNNNVGPIIRAGDLVEPVIETAEIDNPGKEITVEDRRAYVRIAAEGELILTRKTLEEQLGRPFNMQELEINLASFAGQIQADEDQIRFYFDKTM

Source Source

Source organism organism	Pseudomonas mendocina
NCBI taxonomy ID ncbi_taxonomy_id	300
Host organism host_organism	Escherichia coli

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	2

Entity 6 Entity 6 non-polymer

Description description	PHENOL
Molecular weight formula_weight	94.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	611

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3q3oa_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.2 — Ribonucleotide reductase-like

Domain ID domain_id	d3q3oc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.12 — TmoB-like
Family Family family	d.15.12.0 — automated matches

Domain ID domain_id	d3q3oe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.137 — Monooxygenase (hydroxylase) regulatory protein
Superfamily Superfamily superfamily	d.137.1 — Monooxygenase (hydroxylase) regulatory protein
Family Family family	d.137.1.1 — Monooxygenase (hydroxylase) regulatory protein

CATH v4.4 (4 domains)

Domain ID domain_id	3q3oA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	3q3oB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	3q3oC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	270 — TmoB-like

Domain ID domain_id	3q3oE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	56 — Phenol Hydroxylase P2 Protein
Homologous superfamily homologous superfamily	10 — Monooxygenase component MmoB/DmpM

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Unit-cell length a length_a	98.698 Å
Unit-cell length b length_b	116.393 Å
Unit-cell length c length_c	180.789 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	31.659 Å
R factor r_factor	0.1521
R_work r_work	0.1499
R_free r_free	0.1920

Toluene 4 monooxygenase HD complex with phenol

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

Toluene-4-monooxygenase system protein A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Toluene-4-monooxygenase system protein E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Toluene-4-monooxygenase system protein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Toluene-4-monooxygenase system protein D

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

3q3o__assembly_1__model_1

3q3o__assembly_1__model_1 | I(q)

3q3o__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 (8)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)