5aew

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl

Method: X-RAY DIFFRACTION

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

BIPHENYL DIOXYGENASE SUBUNIT ALPHA

BURKHOLDERIA XENOVORANS LB400

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 SUBUNIT BETA × 3 （P37334） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT BETA × 3 （P37334） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 3 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT BETA × 3 （P37334） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT BETA × 3 （P37334） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT BETA × 3 （P37334） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BPHA_BURXL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–459； UniProt 1–459 Author chain C； PDBConstruct 1–459； UniProt 1–459 Author chain E； PDBConstruct 1–459； UniProt 1–459 Author chain G； PDBConstruct 1–459； UniProt 1–459 Author chain I； PDBConstruct 1–459； UniProt 1–459 Author chain K； PDBConstruct 1–459； UniProt 1–459 Author chain M； PDBConstruct 1–459； UniProt 1–459 Author chain O； PDBConstruct 1–459； UniProt 1–459 Author chain Q； PDBConstruct 1–459； UniProt 1–459 Author chain S； PDBConstruct 1–459； UniProt 1–459 Author chain U； PDBConstruct 1–459； UniProt 1–459 Author chain W； PDBConstruct 1–459； UniProt 1–459

BIPHENYL DIOXYGENASE SUBUNIT BETA

BURKHOLDERIA XENOVORANS LB400

UniProt P37334

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 SUBUNIT ALPHA × 3 （P37333） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT ALPHA × 3 （P37333） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 3 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT ALPHA × 3 （P37333） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT ALPHA × 3 （P37333） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	BIPHENYL DIOXYGENASE SUBUNIT ALPHA × 3 （P37333） FE2/S2 (INORGANIC) CLUSTER × 3 FE (II) ION × 3 BIPHENYL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BPHE_BURXL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–188； UniProt 1–188 Author chain D； PDBConstruct 1–188； UniProt 1–188 Author chain F； PDBConstruct 1–188； UniProt 1–188 Author chain H； PDBConstruct 1–188； UniProt 1–188 Author chain J； PDBConstruct 1–188； UniProt 1–188 Author chain L； PDBConstruct 1–188； UniProt 1–188 Author chain N； PDBConstruct 1–188； UniProt 1–188 Author chain P； PDBConstruct 1–188； UniProt 1–188 Author chain R； PDBConstruct 1–188； UniProt 1–188 Author chain T； PDBConstruct 1–188； UniProt 1–188 Author chain V； PDBConstruct 1–188； UniProt 1–188 Author chain X； PDBConstruct 1–188； UniProt 1–188

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	5aew
Deposition date deposition_date	2015-01-10
Structure title title	Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl
Keywords keywords	OXIDOREDUCTASE, BIPHENYL DIOXYGENASE, BPHAE-II9, BIPHENYL, POLYCHLORINATED BIPHENYLS; 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.

5aew__assembly_1__model_1

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

Download this curve (.dat)

5aew__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5aew__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.69 Å
Rg (electron density)	34.73 Å
Total Rg	35.34 Å
Atom count	14809
Residues	1838
Excluded volume	261350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5aew__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5aew__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5aew__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5aew__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5aew__assembly_5__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 SUBUNIT ALPHA
Molecular weight formula_weight	51471.3 kDa
EC 编号 ec_number	1.14.12.18
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q,S,U,W
Atom count atom_count	63519

MSSAIKEVQGAPVKWVTNWTPEAIRGLVDQEKGLLDPRIYADQSLYELELERVFGRSWLLLGHESHVPETGDFLATYMGEDPVVMVRQKDKSIKVFLNQCRHRGMRICRSDAGNAKAFTCSYHGWAYDIAGKLVNVPFEKEAFCDKKEGDCGFDKAEWGPLQARVATYKGLVFANWDVQAPDLETYLGDARPYMDVMLDRTPAGTVAIGGMQKWVIPCNWKFAAEQFCSDMYHAGTTTHLSGILAGIPPEMDLSQAQIPTKGNQFRAAWGGHGSGWYVDEPGSLLAVMGPKVTQYWTEGPAAELAEQRLGHTGMPVRRMVGQHMTIFPTCSFLPGINTIRTWHPRGPNEIEVWAFTLVDADAPAEIKEEYRRHNIRNFSAGGVFEQDDGENWVEIQKGLRGYKAKSQPLNAQMGLGRSQTGHPDFPGNVGYVYAEEAARGMYHHWMRMMSEPSWATLKP

Source Source

Source organism organism	BURKHOLDERIA XENOVORANS LB400
NCBI taxonomy ID ncbi_taxonomy_id	266265
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	BIPHENYL DIOXYGENASE SUBUNIT BETA
Molecular weight formula_weight	22113.8 kDa
EC 编号 ec_number	1.14.12.18
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R,T,V,X

MTNPSPHFFKTFEWPSKAAGLELQNEIEQFYYREAQLLDHRAYEAWFALLDKDIHYFMPLRTNRMIREGELEYSGDQDLAHFDETHETMYGRIRKVTSDVGWAENPPSRTRHLVSNVIVKETATPDTFEVNSAFILYRNRLERQVDIFAGERRDVLRRADNNLGFSIAKRTILLDASTLLSNNLSMFF

Source Source

Source organism organism	BURKHOLDERIA XENOVORANS LB400
NCBI taxonomy ID ncbi_taxonomy_id	266265
Host organism host_organism	ESCHERICHIA COLI

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	12

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	12

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	9

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4017

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6. Fold Classification (SCOP + CATH) 72 domains

SCOP 2.08 (36 domains)

Domain ID domain_id	d5aewa1
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	d5aewa2
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	d5aewb_
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	d5aewc1
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	d5aewc2
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	d5aewd_
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	d5aewe1
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	d5aewe2
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	d5aewf_
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	d5aewg1
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	d5aewg2
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	d5aewh_
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	d5aewi1
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	d5aewi2
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	d5aewj_
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	d5aewk1
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	d5aewk2
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	d5aewl_
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	d5aewm1
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	d5aewm2
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	d5aewn_
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	d5aewo1
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	d5aewo2
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	d5aewp_
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	d5aewq1
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	d5aewq2
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	d5aewr_
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	d5aews1
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	d5aews2
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	d5aewt_
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	d5aewu1
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	d5aewu2
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	d5aewv_
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	d5aeww1
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	d5aeww2
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	d5aewx_
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 (36 domains)

Domain ID domain_id	5aewA01
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	5aewA02
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	5aewB00
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	5aewC01
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	5aewC02
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	5aewD00
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	5aewE01
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	5aewE02
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	5aewF00
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	5aewG01
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	5aewG02
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	5aewH00
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	5aewI01
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	5aewI02
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	5aewJ00
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	5aewK01
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	5aewK02
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	5aewL00
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	5aewM01
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	5aewM02
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	5aewN00
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	5aewO01
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	5aewO02
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	5aewP00
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	5aewQ01
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	5aewQ02
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	5aewR00
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	5aewS01
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	5aewS02
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	5aewT00
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	5aewU01
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	5aewU02
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	5aewV00
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	5aewW01
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	5aewW02
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	5aewX00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

▶

Unit-cell length a length_a	132.767 Å
Unit-cell length b length_b	133.191 Å
Unit-cell length c length_c	133.965 Å
Unit-cell angle α angle_alpha	102.31 °
Unit-cell angle β angle_beta	102.54 °
Unit-cell angle γ angle_gamma	104.54 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	23.340 Å
R factor r_factor	0.2268
R_work r_work	0.2248
R_free r_free	0.2630

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl

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

BIPHENYL DIOXYGENASE SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

BIPHENYL DIOXYGENASE SUBUNIT BETA

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

5aew__assembly_1__model_1

5aew__assembly_1__model_1 | I(q)

5aew__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) 72 domains

SCOP 2.08 (36 domains)

CATH v4.4 (36 domains)

7. Citations (1)

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl

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

BIPHENYL DIOXYGENASE SUBUNIT ALPHA

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 SUBUNIT BETA

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

5aew__assembly_1__model_1

5aew__assembly_1__model_1 | I(q)

5aew__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) 72 domains

SCOP 2.08 (36 domains)

CATH v4.4 (36 domains)

7. Citations (1)