3gkq

Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1

Method: X-RAY DIFFRACTION

▼

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

Terminal oxygenase component of carbazole 1,9a-dioxygenase

Sphingomonas

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	FE (II) ION × 6 FE2/S2 (INORGANIC) CLUSTER × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	FE (II) ION × 6 FE2/S2 (INORGANIC) CLUSTER × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2PFA6_9SPHN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–383； UniProt 1–383 Author chain B； PDBConstruct 1–383； UniProt 1–383 Author chain C； PDBConstruct 1–383； UniProt 1–383 Author chain D； PDBConstruct 1–383； UniProt 1–383 Author chain E； PDBConstruct 1–383； UniProt 1–383 Author chain F； PDBConstruct 1–383； UniProt 1–383

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gkq
Deposition date deposition_date	2009-03-11
Structure title title	Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1
Keywords keywords	Rieske nonheme iron oxygenase, electron transfer, putidaredoxin-type ferredoxin, Dioxygenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3gkq__assembly_1__model_1

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

Download this curve (.dat)

3gkq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gkq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.43 Å
Rg (electron density)	35.66 Å
Total Rg	36.21 Å
Atom count	8961
Residues	1122
Excluded volume	158300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gkq__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gkq__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Terminal oxygenase component of carbazole 1,9a-dioxygenase
Molecular weight formula_weight	43997.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	20106

MQTASVPAGIAERRTRAWAPYIDAKLGFRNHWYPVRLSAEVAEASPVPVQLLGEKVLLNRVDGVVHAIADRCLHRGVTLSDKVECYSKATISCWYHGWTYRWDNGKLVDILTNPTSVQIGRHALKTYPVREEKGLVFLFVGDQEPHDLAEDVPPGFLDADLAVHGQHRVVDANWRMGVENGFDAGHVFIHKSSILLDGNDIALPLGFAPGDPEQLTRSVTGEGAPKGVFDLLGEHSVPIFEATIEGQPAIQGHMGSKMVAISISVWLPGVLKVDPFPDPTLTQFEWYVPIDEGHHLYLQMLGRRVGSEEEARSFEAEFREKWVELALNGFNDDDILARRSMEPFYADDRGWREEVLFESDRAIIEWRRLASQYNRGIQTRDVRHHHHHH

Source Source

Source organism organism	Sphingomonas
NCBI taxonomy ID ncbi_taxonomy_id	164608
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	12

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	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2208

▼

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	3gkqA01
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	3gkqA02
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	3gkqA03
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	3gkqB01
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	3gkqB02
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	3gkqB03
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	3gkqC01
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	3gkqC02
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	3gkqC03
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	3gkqD01
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	3gkqD02
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	3gkqD03
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	3gkqE01
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	3gkqE02
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	3gkqE03
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	3gkqF01
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	3gkqF02
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	3gkqF03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	117.147 Å
Unit-cell length b length_b	159.019 Å
Unit-cell length c length_c	167.774 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	47.070 Å
R factor r_factor	0.2144
R_work r_work	0.2012
R_free r_free	0.4360

Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1

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

Terminal oxygenase component of carbazole 1,9a-dioxygenase

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

3gkq__assembly_1__model_1

3gkq__assembly_1__model_1 | I(q)

3gkq__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1

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

Terminal oxygenase component of carbazole 1,9a-dioxygenase

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

3gkq__assembly_1__model_1

3gkq__assembly_1__model_1 | I(q)

3gkq__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)