2bmq

The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene

Method: X-RAY DIFFRACTION

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

OXYGENASE-ALPHA NBDO

COMAMONAS SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	OXYGENASE-BETA NBDO × 3 （Q8RTL3） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 3 NITROBENZENE × 3 1,2-ETHANEDIOL × 18 ETHANOL × 18 NICKEL (II) ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RTL4_9BURK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–447； UniProt 1–447

OXYGENASE-BETA NBDO

COMAMONAS SP.

UniProt Q8RTL3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	OXYGENASE-ALPHA NBDO × 3 （Q8RTL4） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 3 NITROBENZENE × 3 1,2-ETHANEDIOL × 18 ETHANOL × 18 NICKEL (II) ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RTL3_9BURK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–194； UniProt 1–194

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	2bmq
Deposition date deposition_date	2005-03-15
Structure title title	The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene
Keywords keywords	;NITROBENZENE DIOXYGENASE, NITROARENE, RIESKE NON-HEME DIOXYGENASE, SUBSTRATE SPECIFICITY IRON-SULFUR, METAL-BINDING, NAD, 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.

2bmq__assembly_1__model_1

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

Download this curve (.dat)

2bmq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bmq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.96 Å
Rg (electron density)	35.08 Å
Total Rg	35.71 Å
Atom count	15318
Residues	1893
Excluded volume	271030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bmq__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Description description	OXYGENASE-ALPHA NBDO
Molecular weight formula_weight	49614.5 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	5971

MSYQNLVSEAGLTQKLLIHGDKELFQHELKTIFARNWLFLTHDSLIPSPGDYVKAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVHAEAGNAKGFVCGYHGWGYGSNGELQSVPFEKELYGDAIKKKCLGLKEVPRIESFHGFIYGCFDAEAPPLIDYLGDAAWYLEPTFKYSGGLELVGPPGKVVVKANWKSFAENFVGDGYHVGWTHAAALRAGQSVFSSIAGNAKLPPEGAGLQMTSKYGSGMGVFWGYYSGNFSADMIPDLMAFGAAKQEKLAKEIGDVRARIYRSFLNGTIFPNNSFLTGSAAFRVWNPIDENTTEVWTYAFVEKDMPEDLKRRVADAVQRSIGPAGFWESDDNENMETMSQNGKKYQSSNIDQIASLGFGKDVYGDECYPGVVGKSAIGETSYRGFYRAYQAHISSSNWAEFENASRNWHIEHTKTTDR

Source Source

Source organism organism	COMAMONAS SP.
NCBI taxonomy ID ncbi_taxonomy_id	58226
Host organism host_organism	Escherichia coli DH5[alpha]

Entity 2 Entity 2 polymer

Description description	OXYGENASE-BETA NBDO
Molecular weight formula_weight	23122.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMINTQEDKLVSAHDAEEFHRFFVGHDSDLQQEVTTLLTREAHLLDIQAYKAWLEHFVAPEIKYQVISRELRSTSERRYQLNDAVNLYNENYQQLKVRVEHQMDPQNWANNPKIRFTRFVTNVTAAKDKSAPEILHVRSNLILHRARRENQVDVFYATREDKWKRIEGGGIKLVERFVDYPERIPQTHNLLVFL

Source Source

Source organism organism	COMAMONAS SP.
NCBI taxonomy ID ncbi_taxonomy_id	58226
Host organism host_organism	Escherichia coli DH5[alpha]

Entity 3 Entity 3 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 4 Entity 4 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 5 Entity 5 non-polymer

Description description	NITROBENZENE
Molecular weight formula_weight	123.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	ETHANOL
Molecular weight formula_weight	46.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	699

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2bmqa1
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.33.1.2 — Ring hydroxylating alpha subunit ISP domain

Domain ID domain_id	d2bmqa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.3 — Bet v1-like
Family Family family	d.129.3.3 — Ring hydroxylating alpha subunit catalytic domain

Domain ID domain_id	d2bmqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.4 — Ring hydroxylating beta subunit

CATH v4.4 (3 domains)

Domain ID domain_id	2bmqA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1

Domain ID domain_id	2bmqA02
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	2bmqB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	121.533 Å
Unit-cell length b length_b	121.533 Å
Unit-cell length c length_c	84.179 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	27.000 Å
R factor r_factor	0.1690
R_work r_work	0.1670
R_free r_free	0.1920

The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene

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

OXYGENASE-ALPHA NBDO

State in the Current Structure

Other States of the Same Protein in the Database

OXYGENASE-BETA NBDO

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

2bmq__assembly_1__model_1

2bmq__assembly_1__model_1 | I(q)

2bmq__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene

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

OXYGENASE-ALPHA NBDO

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

OXYGENASE-BETA NBDO

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

2bmq__assembly_1__model_1

2bmq__assembly_1__model_1 | I(q)

2bmq__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)