5tdv

Intermediate O2 diiron complex in the Q228A variant of Toluene 4-moonoxygenase (T4moHD)

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） PEROXIDE ION × 2 FE (III) ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TMOA_PSEME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–500； UniProt 1–500 Author chain D； 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 （Q00456） Toluene-4-monooxygenase system protein B × 2 （Q00457） Toluene-4-monooxygenase system protein D × 2 （Q00459） PEROXIDE ION × 2 FE (III) ION × 4 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 1–327； UniProt 1–327 Author chain F； PDBConstruct 1–327； UniProt 1–327

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 （Q00456） Toluene-4-monooxygenase system protein E × 2 （Q00460） Toluene-4-monooxygenase system protein D × 2 （Q00459） PEROXIDE ION × 2 FE (III) ION × 4 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 Author chain G； 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 （Q00456） Toluene-4-monooxygenase system protein E × 2 （Q00460） Toluene-4-monooxygenase system protein B × 2 （Q00457） PEROXIDE ION × 2 FE (III) ION × 4 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 Author chain H； 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	5tdv
Deposition date deposition_date	2016-09-19
Structure title title	Intermediate O2 diiron complex in the Q228A variant of Toluene 4-moonoxygenase (T4moHD)
Keywords keywords	diiron, oxygen activation, complex, 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.

5tdv__assembly_1__model_1

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

Download this curve (.dat)

5tdv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tdv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.87 Å
Rg (electron density)	39.39 Å
Total Rg	39.80 Å
Atom count	16009
Residues	1959
Excluded volume	282150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tdv__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 (7)

Entity 1 Entity 1 polymer

Description description	Toluene-4-monooxygenase system protein A
Molecular weight formula_weight	58099.2 kDa
EC 编号 ec_number	1.14.13.-
Mutation mutation	Q228A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	17695

MAMHPRKDWYELTRATNWTPSYVTEEQLFPERMSGHMGIPLEKWESYDEPYKTSYPEYVSIQREKDAGAYSVKAALERAKIYENSDPGWISTLKSHYGAIAVGEYAAVTGEGRMARFSKAPGNRNMATFGMMDELRHGQLQLFFPHEYCKKDRQFDWAWRAYHSNEWAAIAAKHFFDDIITGRDAISVAIMLTFSFETGFTNMQFLGLAADAAEAGDYTFANLISSIATDESRHAQQGGPALQLLIENGKREEAQKKVDMAIWRAWRLFAVLTGPVMDYYTPLEDRSQSFKEFMYEWIIGQFERSLIDLGLDKPWYWDLFLKDIDELHHSYHMGVWYWRTTAWWNPAAGVTPEERDWLEEKYPGWNKRWGRCWDVITENVLDDRMDLVSPETLPSVCNMSQIPLVGVPGDDWNIEVFSLEHNGRLYHFGSEVDRWVFQQDPVQYQNHMNIVDRFLAGQIQPMTLDGALKYMGFQSIEEMGKDAHDFAWADKCKPAMKKSA

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	38410.2 kDa
EC 编号 ec_number	1.14.13.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MSFESKKPMRTWSHLAEMRKKPSEYDIVSRKLHYSTNNPDSPWELSPDSPMNLWYKQYRNASPLKHDNWDAFTDPDQLVYRTYNLMQDGQESYVQSLFDQFNEREHDQMVREGWEHTMARCYSPLRYLFHCLQMSSAYVQQMAPASTISNCCILQTADSLRWLTHTAYRTHELSLTYPDAGLGEHERELWEKEPGWQGLRELMEKQLTAFDWGEAFVSLNLVVKPMIVESIFKPLQQQAYENNDTLLPLLIDSQLKDAERHSRWSKALVKHALENPDNHAVIEGWIEKWRPLADRAAEAYLSMLSSDILHAQYLERSTSLRASILTV

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	2

Polymer Polymer

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

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	11642.1 kDa
EC 编号 ec_number	1.14.13.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,H

MSTLAQQALHNNNVGPIIRAGDLVEPVIETAEIDNPGKEITVEDRRAYVRIAAEGELILTRKTLEEQLGRPFNMQELEINLASFAGQIQADEDQIRFYFDKTM

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	PEROXIDE ION
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1509

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5tdva_
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	d5tdvc_
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	d5tdvd_
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	d5tdve_
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

Domain ID domain_id	d5tdvg_
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	d5tdvh_
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 (8 domains)

Domain ID domain_id	5tdvA00
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	5tdvB00
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	5tdvC00
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	5tdvD00
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	5tdvE00
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

Domain ID domain_id	5tdvF00
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	5tdvG00
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	5tdvH00
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	100.293 Å
Unit-cell length b length_b	115.757 Å
Unit-cell length c length_c	181.654 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.001 Å
Low-resolution limit resolution_low	42.276 Å
R factor r_factor	0.1550
R_work r_work	0.1529
R_free r_free	0.1950

Intermediate O2 diiron complex in the Q228A variant of Toluene 4-moonoxygenase (T4moHD)

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

5tdv__assembly_1__model_1

5tdv__assembly_1__model_1 | I(q)

5tdv__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 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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)