1ulj

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

Method: X-RAY DIFFRACTION

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

biphenyl dioxygenase large subunit

Rhodococcus sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	biphenyl dioxygenase small subunit × 3 （Q53123） FE (II) ION × 3 FE2/S2 (INORGANIC) CLUSTER × 3 BIPHENYL × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53122_RHOSR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 1–460 Author chain C； PDBConstruct 1–460； UniProt 1–460 Author chain E； PDBConstruct 1–460； UniProt 1–460

biphenyl dioxygenase small subunit

Rhodococcus sp.

UniProt Q53123

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	biphenyl dioxygenase large subunit × 3 （Q53122） FE (II) ION × 3 FE2/S2 (INORGANIC) CLUSTER × 3 BIPHENYL × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53123_RHOSR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–187； UniProt 1–187 Author chain D； PDBConstruct 1–187； UniProt 1–187 Author chain F； PDBConstruct 1–187； UniProt 1–187

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	1ulj
Deposition date deposition_date	2003-09-12
Structure title title	Biphenyl dioxygenase (BphA1A2) in complex with the substrate
Keywords keywords	alpha3 beta3 hetero hexamer, 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.

1ulj__assembly_1__model_1

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

Download this curve (.dat)

1ulj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ulj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.52 Å
Rg (electron density)	34.46 Å
Total Rg	35.04 Å
Atom count	14637
Residues	1807
Excluded volume	257220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ulj__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	biphenyl dioxygenase large subunit
Molecular weight formula_weight	51644.6 kDa
EC 编号 ec_number	1.14.12.18
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	14936

MTDVQCEPALAGRKPKWADADIAELVDERTGRLDPRIYTDEALYEQELERIFGRSWLLMGHETQIPKAGDFMTNYMGEDPVMVVRQKNGEIRVFLNQCRHRGMRICRADGGNAKSFTCSYHGWAYDTGGNLVSVPFEEQAFPGLRKEDWGPLQARVETYKGLIFANWDADAPDLDTYLGEAKFYMDHMLDRTEAGTEAIPGIQKWVIPCNWKFAAEQFCSDMYHAGTTSHLSGILAGLPDGVDLSELAPPTEGIQYRATWGGHGSGFYIGDPNLLLAIMGPKVTEYWTQGPAAEKASERLGSTERGQQLMAQHMTIFPTCSFLPGINTIRAWHPRGPNEIEVWAFTVVDADAPEEMKEEYRQQTLRTFSAGGVFEQDDGENWVEIQQVLRGHKARSRPFNAEMGLGQTDSDNPDYPGTISYVYSEEAARGLYTQWVRMMTSPDWAALDATRPAVSESTHT

Source Source

Source organism organism	Rhodococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	101510
Host organism host_organism	Rhodococcus erythropolis

Entity 2 Entity 2 polymer

Description description	biphenyl dioxygenase small subunit
Molecular weight formula_weight	22049.8 kDa
EC 编号 ec_number	1.14.12.18
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MIDAESPTTAFRTKPAPVDPSLQHEIEQFYYWEAKLLNDRRFQEWFDLLAEDIHYFMPIRTTRIMRETAQEYSGAREYAHFDDNAQMMRGRLRKITSDVSWSENPASRTRHVISNVMIVDGEKPGEYHVSSVFIVYRNRLERQLDIFAGERKDILRRTGSEAGFELAKRTILIDQSTILSNNLSFFF

Source Source

Source organism organism	Rhodococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	101510
Host organism host_organism	Rhodococcus erythropolis

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	3

Entity 5 Entity 5 non-polymer

Description description	BIPHENYL
Molecular weight formula_weight	154.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	299

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1ulja1
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	d1ulja2
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	d1uljb_
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	d1uljc1
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	d1uljc2
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	d1uljd_
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	d1ulje1
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	d1ulje2
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	d1uljf_
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

CATH v4.4 (9 domains)

Domain ID domain_id	1uljA01
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	1uljA02
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	1uljB00
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	1uljC01
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	1uljC02
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	1uljD00
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	1uljE01
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	1uljE02
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	1uljF00
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	137.834 Å
Unit-cell length b length_b	137.834 Å
Unit-cell length c length_c	237.960 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	36.760 Å
R factor r_factor	0.1860
R_work r_work	0.1835
R_free r_free	0.2336

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

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

biphenyl dioxygenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

biphenyl 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

1ulj__assembly_1__model_1

1ulj__assembly_1__model_1 | I(q)

1ulj__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

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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (2)

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

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

biphenyl 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

biphenyl 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

1ulj__assembly_1__model_1

1ulj__assembly_1__model_1 | I(q)

1ulj__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

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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (2)