6llf

Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase

Method: X-RAY DIFFRACTION

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

Terminal oxygenase component of carbazole

Janthinobacterium sp. (strain J3)

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） FE2/S2 (INORGANIC) CLUSTER × 6 FE (II) ION × 3 3-(2-hydroxyphenyl)benzene-1,2-diol × 3 1,2-ETHANEDIOL × 17 GLYCEROL × 4 TRIETHYLENE GLYCOL × 1 DI(HYDROXYETHYL)ETHER × 1 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） FE2/S2 (INORGANIC) CLUSTER × 6 FE (II) ION × 3 3-(2-hydroxyphenyl)benzene-1,2-diol × 3 1,2-ETHANEDIOL × 17 GLYCEROL × 4 TRIETHYLENE GLYCOL × 1 DI(HYDROXYETHYL)ETHER × 1 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	6llf
Deposition date deposition_date	2019-12-23
Structure title title	Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase
Keywords keywords	complex, dioxygenase, ligand-bound, 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.

6llf__assembly_1__model_1

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

Download this curve (.dat)

6llf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6llf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.97 Å
Rg (electron density)	38.25 Å
Total Rg	38.71 Å
Atom count	11896
Residues	1479
Excluded volume	211450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6llf__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 (10)

Entity 1 Entity 1 polymer

Description description	Terminal oxygenase component of carbazole
Molecular weight formula_weight	44910.7 kDa
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	13321

MANVDEAILKRVKGWAPYVDAKLGFRNHWYPVMFSKEINEGEPKTLKLLGENLLVNRIDGKLYCLKDRCLHRGVQLSVKVECKTKSTITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGDGDPPPLARDTPPNFLDDDMEILGKNQIIKSNWRLAVENGFDPSHIYIHKDSILVKDNDLALPLGFAPGGDRKQQTRVVDDDVVGRKGVYDLIGEHGVPVFEGTIGGEVVREGAYGEKIVANDISIWLPGVLKVNPFPNPDMMQFEWYVPIDENTHYYFQTLGKPCANDEERKKYEQEFESKWKPMALEGFNNDDIWAREAMVDFYADDKGWVNEILFESDEAIVAWRKLASEHNQGIQTQAHVSGLEHHHHHH

Source Source

Source organism organism	Janthinobacterium sp. (strain J3)
NCBI taxonomy ID ncbi_taxonomy_id	213804
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ferredoxin CarAc
Molecular weight formula_weight	12448.1 kDa
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 BL21(DE3)

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 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 5 Entity 5 non-polymer

Description description	3-(2-hydroxyphenyl)benzene-1,2-diol
Molecular weight formula_weight	202.2 kDa
Source method src_method	syn
Copy count entity_count	3

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	17

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1297

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d6llfa1
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.33.1.0 — automated matches

Domain ID domain_id	d6llfa2
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	d6llfa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6llfb1
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.33.1.0 — automated matches

Domain ID domain_id	d6llfb2
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	d6llfb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6llfc1
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.33.1.0 — automated matches

Domain ID domain_id	d6llfc2
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	d6llfc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	98.294 Å
Unit-cell length b length_b	89.684 Å
Unit-cell length c length_c	105.021 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.08 °
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	1.930 Å
Low-resolution limit resolution_low	44.880 Å
R factor r_factor	0.1603
R_work r_work	0.1583
R_free r_free	0.2002

Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase

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

6llf__assembly_1__model_1

6llf__assembly_1__model_1 | I(q)

6llf__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 (10)

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

7. Citations (1)

Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase

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

6llf__assembly_1__model_1

6llf__assembly_1__model_1 | I(q)

6llf__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 (10)

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

7. Citations (1)