2b1x

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.

Method: X-RAY DIFFRACTION

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

naphthalene dioxygenase large subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	naphthalene dioxygenase small subunit × 3 （Q9WVZ0） FE (III) ION × 3 FE2/S2 (INORGANIC) CLUSTER × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 13 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X3R9_9NOCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–470； UniProt 1–470 Author chain C； PDBConstruct 1–470； UniProt 1–470 Author chain E； PDBConstruct 1–470； UniProt 1–470

naphthalene dioxygenase small subunit

OrganismNot specified

UniProt Q9WVZ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	naphthalene dioxygenase large subunit × 3 （Q9X3R9） FE (III) ION × 3 FE2/S2 (INORGANIC) CLUSTER × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 13 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WVZ0_9NOCA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–172； UniProt 1–172 Author chain D； PDBConstruct 1–172； UniProt 1–172 Author chain F； PDBConstruct 1–172； UniProt 1–172

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	2b1x
Deposition date deposition_date	2005-09-16
Structure title title	Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.
Keywords keywords	RIESKE NON-HEME IRON OXYGENASE, 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.

2b1x__assembly_1__model_1

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

Download this curve (.dat)

2b1x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b1x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.87 Å
Rg (electron density)	35.01 Å
Total Rg	35.45 Å
Atom count	14681
Residues	1824
Excluded volume	259620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b1x__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 (6)

Entity 1 Entity 1 polymer

Description description	naphthalene dioxygenase large subunit
Molecular weight formula_weight	52580.9 kDa
EC 编号 ec_number	1.14.12.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	15793

MLSNELRQTLQKGLHDVNSDWTVPAAIINDPEVHDVERERIFGHAWVFLAHESEIPERGDYVVRYISEDQFIVCRDEGGEIRGHLNACRHRGMQVCRAEMGNTSHFRCPYHGWTYSNTGSLVGVPAGKDAYGNQLKKSDWNLRPMPNLASYKGLIFGSLDPHADSLEDYLGDLKFYLDIVLDRSDAGLQVVGAPQRWVIDANWKLGADNFVGDAYHTMMTHRSMVELGLAPPDPQFALYGEHIHTGHGHGLGIIGPPPGMPLPEFMGLPENIVEELERRLTPEQVEIFRPTAFIHGTVFPNLSIGNFLMGKDHLSAPTAFLTLRLWHPLGPDKMEVMSFFLVEKDAPDWFKDESYKSYLRTFGISGGFEQDDAENWRSITRVMGGQFAKTGELNYQMGRGVLEPDPNWTGPGEAYPLDYAEANQRNFLEYWMQLMLAESPLRDGNSNGSGTADASTPAAAKSKSPAKAEA

Entity 2 Entity 2 polymer

Description description	naphthalene dioxygenase small subunit
Molecular weight formula_weight	19836.4 kDa
EC 编号 ec_number	1.14.12.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MNTQTRVSDTTVREITEWLYMEAELLDAGKYREWLALVTEDLSYVVPIRVTREREAVTDVVEGMTHMDDDADSMEMRVLRLETEYAWAEDPPSRSRHFVTNVRVATGDSEDEFKVTSNLLLYRTRGDVATYDVLSGERTDVLRRAGDSFLMAKRVVLLDQTTIMTHNLALIM

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	3

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	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1112

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2b1xa1
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	d2b1xa2
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	d2b1xb1
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

Domain ID domain_id	d2b1xc1
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	d2b1xc2
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	d2b1xd_
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.17.4.0 — automated matches

Domain ID domain_id	d2b1xe1
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	d2b1xe2
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	d2b1xf_
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.17.4.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id	2b1xA01
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	2b1xA02
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	2b1xB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2b1xC01
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	2b1xC02
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	2b1xD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2b1xE01
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	2b1xE02
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	2b1xF00
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	87.744 Å
Unit-cell length b length_b	144.246 Å
Unit-cell length c length_c	186.207 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.800 Å
R factor r_factor	0.1913
R_work r_work	0.1906
R_free r_free	0.2243

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.

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

naphthalene dioxygenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

naphthalene dioxygenase small subunit

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

2b1x__assembly_1__model_1

2b1x__assembly_1__model_1 | I(q)

2b1x__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.

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

naphthalene dioxygenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

naphthalene dioxygenase small subunit

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

2b1x__assembly_1__model_1

2b1x__assembly_1__model_1 | I(q)

2b1x__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)