2ckf

Crystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from Sphingomonas sp CHY-1

Method: X-RAY DIFFRACTION

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

RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT

SPHINGOMONAS SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT × 3 （Q65AT0） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q65AT1_9SPHN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–454； UniProt 1–454 Author chain C； PDBConstruct 1–454； UniProt 1–454 Author chain E； PDBConstruct 1–454； UniProt 1–454

RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT

SPHINGOMONAS SP.

UniProt Q65AT0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT × 3 （Q65AT1） FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q65AT0_9SPHN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–174； UniProt 1–174 Author chain D； PDBConstruct 1–174； UniProt 1–174 Author chain F； PDBConstruct 1–174； UniProt 1–174

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	2ckf
Deposition date deposition_date	2006-04-18
Structure title title	Crystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from Sphingomonas sp CHY-1
Keywords keywords	;RIESKE NON HEME IRON DIOXYGENASE, PYRENE DIOXYGENASE, RING-HYDROXYLATING DIOXYGENASE, HIGH-MOLECULAR-WEIGHT POLYCYCLIC AROMATIC HYDROCARBONS, 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.

2ckf__assembly_1__model_1

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

Download this curve (.dat)

2ckf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ckf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.39 Å
Rg (electron density)	35.39 Å
Total Rg	35.85 Å
Atom count	14692
Residues	1816
Excluded volume	257670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ckf__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	RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT
Molecular weight formula_weight	50847.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	15833

MSGDTTLVDTVNASQSRQVFWDRDVYDLEIERIFSRAWLMLGHKSLLPKPGDFITTYMAEDKIILSHQSDGTFRAFINSCTHRGNQICHADSGNAKAFVCNYHGWVYGQDGSLVDVPLESRCYHNKLDKQELAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRFYLDTIWEGGGAGLELLGPPMKSLLHCNWKVPVENFVGDGYHVGWTHAAALGQIGGPLAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAAIHRKGDGWNKYLEDTRGEVRRKFGADRERLYVGHWNGAIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTMVPSDADPATKSAIQREATRTFGTAGTLESDDGENMSSATYVNRGVITRDGMMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDNWDSVFTNRNFWNEKLNAAE

Source Source

Source organism organism	SPHINGOMONAS SP.
NCBI taxonomy ID ncbi_taxonomy_id	279135
Host organism host_organism	PSEUDOMONAS PUTIDA

Entity 2 Entity 2 polymer

Description description	RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT
Molecular weight formula_weight	20833.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MSTEQVPVTPDVHYAVEAHYRAEVRLLQTGQYREWLHGMVAEDIHYWMPIYEQRFVRDRRPDPTPDDAAIYNDDFEELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAENGELDVLSNILVYRNRRQTEVTVHTLGREDKLRQDGNGFKVFRRKLILDARVTQDKNLYFFC

Source Source

Source organism organism	SPHINGOMONAS SP.
NCBI taxonomy ID ncbi_taxonomy_id	279135
Host organism host_organism	PSEUDOMONAS PUTIDA

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	3

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	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1096

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2ckfa1
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	d2ckfa2
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.129.3.0 — automated matches

Domain ID domain_id	d2ckfb_
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	d2ckfc1
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	d2ckfc2
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.129.3.0 — automated matches

Domain ID domain_id	d2ckfd_
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	d2ckfe1
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	d2ckfe2
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.129.3.0 — automated matches

Domain ID domain_id	d2ckff_
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	2ckfA01
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	2ckfA02
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	2ckfB00
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	2ckfC01
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	2ckfC02
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	2ckfD00
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	2ckfE01
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	2ckfE02
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	2ckfF00
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	92.644 Å
Unit-cell length b length_b	112.730 Å
Unit-cell length c length_c	190.626 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	1.850 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2360

Crystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from Sphingomonas sp CHY-1

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

RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

RING-HYDROXYLATING DIOXYGENASE BETA 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

2ckf__assembly_1__model_1

2ckf__assembly_1__model_1 | I(q)

2ckf__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) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from Sphingomonas sp CHY-1

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

RING-HYDROXYLATING DIOXYGENASE ALPHA 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

RING-HYDROXYLATING DIOXYGENASE BETA 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

2ckf__assembly_1__model_1

2ckf__assembly_1__model_1 | I(q)

2ckf__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) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)