2iga

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

Method: X-RAY DIFFRACTION

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

Homoprotocatechuate 2,3-dioxygenase

Brevibacterium fuscum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FE (II) ION × 4 CHLORIDE ION × 4 2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID × 1 GLYCEROL × 13 CALCIUM ION × 1 (1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE × 2 1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED × 1 OXYGEN MOLECULE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q45135_9MICO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–365； UniProt 1–365 Author chain B； PDBConstruct 1–365； UniProt 1–365 Author chain C； PDBConstruct 1–365； UniProt 1–365 Author chain D； PDBConstruct 1–365； UniProt 1–365

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	2iga
Deposition date deposition_date	2006-09-22
Structure title title	Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.
Keywords keywords	;oxygenase, extradiol, Fe(II), homoprotocatechuate, alkylperoxo intermediate, substrate-semiquinone, open-ring product, 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.

2iga__assembly_1__model_1

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

Download this curve (.dat)

2iga__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iga__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.40 Å
Rg (electron density)	32.56 Å
Total Rg	33.22 Å
Atom count	11689
Residues	1436
Excluded volume	204860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iga__assembly_1__model_1`	tetrameric （4）	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	Homoprotocatechuate 2,3-dioxygenase
Molecular weight formula_weight	41755.3 kDa
EC 编号 ec_number	1.13.11.15
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12927

MSNEIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLGNQL

Source Source

Source organism organism	Brevibacterium fuscum
NCBI taxonomy ID ncbi_taxonomy_id	47914
Host organism host_organism	Escherichia coli BL21(DE3)

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	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID
Molecular weight formula_weight	187.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	(1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE
Molecular weight formula_weight	187.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED
Molecular weight formula_weight	154.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 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	1042

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2igaa1
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	d2igaa2
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	d2igab1
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	d2igab2
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	d2igac1
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	d2igac2
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	d2igad1
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	d2igad2
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 (12 domains)

Domain ID domain_id	2igaA01
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	2igaA02
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	2igaA03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1270 — homoprotocatechuate 2,3-dioxygenase fold
Homologous superfamily homologous superfamily	10 — homoprotocatechuate 2,3-dioxygenase domains

Domain ID domain_id	2igaB01
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	2igaB02
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	2igaB03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1270 — homoprotocatechuate 2,3-dioxygenase fold
Homologous superfamily homologous superfamily	10 — homoprotocatechuate 2,3-dioxygenase domains

Domain ID domain_id	2igaC01
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	2igaC02
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	2igaC03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1270 — homoprotocatechuate 2,3-dioxygenase fold
Homologous superfamily homologous superfamily	10 — homoprotocatechuate 2,3-dioxygenase domains

Domain ID domain_id	2igaD01
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	2igaD02
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	2igaD03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1270 — homoprotocatechuate 2,3-dioxygenase fold
Homologous superfamily homologous superfamily	10 — homoprotocatechuate 2,3-dioxygenase domains

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Unit-cell length a length_a	110.678 Å
Unit-cell length b length_b	153.022 Å
Unit-cell length c length_c	96.389 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	52.700 Å
R factor r_factor	—
R_work r_work	0.1850
R_free r_free	0.2450

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

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

Homoprotocatechuate 2,3-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

2iga__assembly_1__model_1

2iga__assembly_1__model_1 | I(q)

2iga__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 non-polymer

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) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

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

Homoprotocatechuate 2,3-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

2iga__assembly_1__model_1

2iga__assembly_1__model_1 | I(q)

2iga__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 non-polymer

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) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)