SAXSdb — 1kmy

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

2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE

Burkholderia xenovorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	FE (II) ION × 8 BIPHENYL-2,3-DIOL × 8 TERTIARY-BUTYL ALCOHOL × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BPHC_BURCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297

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	1kmy
Deposition date deposition_date	2001-12-17
Structure title title	Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition
Keywords keywords	dioxygenase, 2, 3-dihydroxybiphenyl, 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.

1kmy__assembly_1__model_1

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

Download this curve (.dat)

1kmy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kmy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.41 Å
Rg (electron density)	39.77 Å
Total Rg	40.31 Å
Atom count	17888
Residues	2304
Excluded volume	317250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kmy__assembly_1__model_1`	octameric （8）	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	2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
Molecular weight formula_weight	32377.6 kDa
EC 编号 ec_number	1.13.11.39
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2451

SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLKQAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFYTDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRHTNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVRDKAAARNKA

Source Source

Source organism organism	Burkholderia xenovorans
NCBI taxonomy ID ncbi_taxonomy_id	266265
Host organism host_organism	Burkholderia cepacia

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	1

Entity 3 Entity 3 non-polymer

Description description	BIPHENYL-2,3-DIOL
Molecular weight formula_weight	186.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	TERTIARY-BUTYL ALCOHOL
Molecular weight formula_weight	74.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kmya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.3 — Extradiol dioxygenases

Domain ID domain_id	d1kmya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.3 — Extradiol dioxygenases

CATH v4.4 (2 domains)

Domain ID domain_id	1kmyA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	1kmyA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

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Unit-cell length a length_a	123.300 Å
Unit-cell length b length_b	123.300 Å
Unit-cell length c length_c	110.900 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1980
R_work r_work	0.1630
R_free r_free	0.1960

Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition

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

2,3-DIHYDROXYBIPHENYL 1,2-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

1kmy__assembly_1__model_1

1kmy__assembly_1__model_1 | I(q)

1kmy__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)

Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition

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

2,3-DIHYDROXYBIPHENYL 1,2-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

1kmy__assembly_1__model_1

1kmy__assembly_1__model_1 | I(q)

1kmy__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)