2rdb

X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant

Method: X-RAY DIFFRACTION

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

Toluene, o-xylene monooxygenase oxygenase subunit;alpha

Pseudomonas stutzeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Toluene, o-xylene monooxygenase oxygenase subunit;beta × 1 （O87802） Toluene, o-xylene monooxygenase oxygenase subunit;gamma × 1 （O87799） GLYCEROL × 2 HEXAETHYLENE GLYCOL × 1 FE (III) ION × 2 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Toluene, o-xylene monooxygenase oxygenase subunit;beta × 2 （O87802） Toluene, o-xylene monooxygenase oxygenase subunit;gamma × 2 （O87799） GLYCEROL × 4 HEXAETHYLENE GLYCOL × 2 FE (III) ION × 4 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87798_PSEST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–498； UniProt 1–498

Toluene, o-xylene monooxygenase oxygenase subunit;beta

Pseudomonas stutzeri

UniProt O87802

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Toluene, o-xylene monooxygenase oxygenase subunit;alpha × 1 （O87798） Toluene, o-xylene monooxygenase oxygenase subunit;gamma × 1 （O87799） GLYCEROL × 2 HEXAETHYLENE GLYCOL × 1 FE (III) ION × 2 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Toluene, o-xylene monooxygenase oxygenase subunit;alpha × 2 （O87798） Toluene, o-xylene monooxygenase oxygenase subunit;gamma × 2 （O87799） GLYCEROL × 4 HEXAETHYLENE GLYCOL × 2 FE (III) ION × 4 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87802_PSEST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–330； UniProt 1–330

Toluene, o-xylene monooxygenase oxygenase subunit;gamma

Pseudomonas stutzeri

UniProt O87799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Toluene, o-xylene monooxygenase oxygenase subunit;alpha × 1 （O87798） Toluene, o-xylene monooxygenase oxygenase subunit;beta × 1 （O87802） GLYCEROL × 2 HEXAETHYLENE GLYCOL × 1 FE (III) ION × 2 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Toluene, o-xylene monooxygenase oxygenase subunit;alpha × 2 （O87798） Toluene, o-xylene monooxygenase oxygenase subunit;beta × 2 （O87802） GLYCEROL × 4 HEXAETHYLENE GLYCOL × 2 FE (III) ION × 4 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87799_PSEST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–86； UniProt 1–86

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	2rdb
Deposition date deposition_date	2007-09-21
Structure title title	X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant
Keywords keywords	diiron, 4-helix bundle, carboxylate bridge, metalloenzyme, tryptophan radical, Monooxygenase, 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.

2rdb__assembly_1__model_1

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

Download this curve (.dat)

2rdb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rdb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.43 Å
Rg (electron density)	29.83 Å
Total Rg	30.45 Å
Atom count	7387
Residues	896
Excluded volume	130230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rdb__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rdb__assembly_2__model_1`	hexameric （6）	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, o-xylene monooxygenase oxygenase subunit;alpha
Molecular weight formula_weight	57859.8 kDa
Mutation mutation	I100W
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	7556

MSMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAWALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYKNHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQKKTNAA

Source Source

Source organism organism	Pseudomonas stutzeri
NCBI taxonomy ID ncbi_taxonomy_id	316
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Toluene, o-xylene monooxygenase oxygenase subunit;beta
Molecular weight formula_weight	38381.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSEQQPEALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMGL

Source Source

Source organism organism	Pseudomonas stutzeri
NCBI taxonomy ID ncbi_taxonomy_id	316
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Toluene, o-xylene monooxygenase oxygenase subunit;gamma
Molecular weight formula_weight	9986.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMDN

Source Source

Source organism organism	Pseudomonas stutzeri
NCBI taxonomy ID ncbi_taxonomy_id	316
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

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	2

Entity 7 Entity 7 non-polymer

Description description	3[N-MORPHOLINO]PROPANE SULFONIC ACID
Molecular weight formula_weight	209.3 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	158

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2rdba_
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	d2rdbb_
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	d2rdbc_
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.15.12.1 — TmoB-like

CATH v4.4 (3 domains)

Domain ID domain_id	2rdbA00
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	2rdbB00
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	2rdbC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	270 — TmoB-like

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Unit-cell length a length_a	182.420 Å
Unit-cell length b length_b	182.420 Å
Unit-cell length c length_c	67.962 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	36.840 Å
R factor r_factor	0.2206
R_work r_work	0.2172
R_free r_free	0.2837

X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant

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

Toluene, o-xylene monooxygenase oxygenase subunit;alpha

State in the Current Structure

Other States of the Same Protein in the Database

Toluene, o-xylene monooxygenase oxygenase subunit;beta

State in the Current Structure

Other States of the Same Protein in the Database

Toluene, o-xylene monooxygenase oxygenase subunit;gamma

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

2rdb__assembly_1__model_1

2rdb__assembly_1__model_1 | I(q)

2rdb__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 non-polymer

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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant

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

Toluene, o-xylene monooxygenase oxygenase subunit;alpha

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, o-xylene monooxygenase oxygenase subunit;beta

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, o-xylene monooxygenase oxygenase subunit;gamma

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

2rdb__assembly_1__model_1

2rdb__assembly_1__model_1 | I(q)

2rdb__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 non-polymer

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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)