4nbc

Oxygenase with Phe275 replaced by Trp and ferredoxin complex of carbazole 1,9a-dioxygenase (form1)

Method: X-RAY DIFFRACTION

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

Terminal oxygenase component of carbazole

Janthinobacterium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Ferredoxin CarAc × 3 （Q8GI16） FE (II) ION × 3 FE2/S2 (INORGANIC) CLUSTER × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84II6_JANS3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–384； UniProt 1–384 Author chain B； PDBConstruct 1–384； UniProt 1–384 Author chain C； PDBConstruct 1–384； UniProt 1–384

Ferredoxin CarAc

Pseudomonas resinovorans

UniProt Q8GI16

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Terminal oxygenase component of carbazole × 3 （Q84II6） FE (II) ION × 3 FE2/S2 (INORGANIC) CLUSTER × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CARAC_PSERE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–107； UniProt 1–107 Author chain E； PDBConstruct 1–107； UniProt 1–107 Author chain F； PDBConstruct 1–107； UniProt 1–107

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	4nbc
Deposition date deposition_date	2013-10-23
Structure title title	Oxygenase with Phe275 replaced by Trp and ferredoxin complex of carbazole 1,9a-dioxygenase (form1)
Keywords keywords	Rieske non-heme iron oxygenase, carbazole 1, 9a-dioxygenase, 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.

4nbc__assembly_1__model_1

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

Download this curve (.dat)

4nbc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nbc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.03 Å
Rg (electron density)	38.31 Å
Total Rg	38.76 Å
Atom count	11732
Residues	1477
Excluded volume	208210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nbc__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 (5)

Entity 1 Entity 1 polymer

Description description	Terminal oxygenase component of carbazole
Molecular weight formula_weight	44949.8 kDa
EC 编号 ec_number	1.14.12.22
Mutation mutation	F275W
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	12980

MANVDEAILKRVKGWAPYVDAKLGFRNHWYPVMFSKEINEGEPKTLKLLGENLLVNRIDGKLYCLKDRCLHRGVQLSVKVECKTKSTITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGDGDPPPLARDTPPNFLDDDMEILGKNQIIKSNWRLAVENGFDPSHIYIHKDSILVKDNDLALPLGFAPGGDRKQQTRVVDDDVVGRKGVYDLIGEHGVPVFEGTIGGEVVREGAYGEKIVANDISIWLPGVLKVNPWPNPDMMQFEWYVPIDENTHYYFQTLGKPCANDEERKKYEQEFESKWKPMALEGFNNDDIWAREAMVDFYADDKGWVNEILFESDEAIVAWRKLASEHNQGIQTQAHVSGLEHHHHHH

Source Source

Source organism organism	Janthinobacterium
NCBI taxonomy ID ncbi_taxonomy_id	213804
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ferredoxin CarAc
Molecular weight formula_weight	12448.1 kDa
EC 编号 ec_number	1.14.12.22
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MNQIWLKVCAASDMQPGTIRRVNRVGAAPLAVYRVGDQFYATEDTCTHGIASLSEGTLDGDVIECPFHGGAFNVCTGMPASSPCTVPLGVFEVEVKEGEVYVAGEKKLEHHHHHH

Source Source

Source organism organism	Pseudomonas resinovorans
NCBI taxonomy ID ncbi_taxonomy_id	53412
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FE (II) 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	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1248

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4nbcA01
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	4nbcA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4nbcA03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4nbcB01
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	4nbcB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4nbcB03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4nbcC01
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	4nbcC02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4nbcC03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4nbcD00
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	4nbcE00
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	4nbcF00
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

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Unit-cell length a length_a	98.495 Å
Unit-cell length b length_b	90.083 Å
Unit-cell length c length_c	105.384 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.945 Å
Low-resolution limit resolution_low	39.280 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2150

Oxygenase with Phe275 replaced by Trp and ferredoxin complex of carbazole 1,9a-dioxygenase (form1)

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

Terminal oxygenase component of carbazole

State in the Current Structure

Other States of the Same Protein in the Database

Ferredoxin CarAc

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

4nbc__assembly_1__model_1

4nbc__assembly_1__model_1 | I(q)

4nbc__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Oxygenase with Phe275 replaced by Trp and ferredoxin complex of carbazole 1,9a-dioxygenase (form1)

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

Terminal oxygenase component of carbazole

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ferredoxin CarAc

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

4nbc__assembly_1__model_1

4nbc__assembly_1__model_1 | I(q)

4nbc__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)