2boy

Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP

Method: X-RAY DIFFRACTION

▼

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

3-CHLOROCATECHOL 1,2-DIOXYGENASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 BENZHYDROXAMIC ACID × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 MAGNESIUM ION × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 BENZHYDROXAMIC ACID × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 MAGNESIUM ION × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 BENZHYDROXAMIC ACID × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 MAGNESIUM ION × 5 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 BENZHYDROXAMIC ACID × 2 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE × 2 MAGNESIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8G9L3_RHOOP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 1–254 Author chain B； PDBConstruct 1–254； UniProt 1–254 Author chain C； PDBConstruct 1–254； UniProt 1–254 Author chain D； PDBConstruct 1–254； UniProt 1–254 Author chain E； PDBConstruct 1–254； UniProt 1–254 Author chain F； PDBConstruct 1–254； UniProt 1–254 Author chain G； PDBConstruct 1–254； UniProt 1–254 Author chain H； PDBConstruct 1–254； UniProt 1–254

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2boy
Deposition date deposition_date	2005-04-15
Structure title title	Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP
Keywords keywords	BETA BARREL, OXIDOREDUCTASE, DIOXYGENASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2boy__assembly_1__model_1

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

Download this curve (.dat)

2boy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2boy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.50 Å
Rg (electron density)	29.86 Å
Total Rg	30.31 Å
Atom count	4014
Residues	505
Excluded volume	71687 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2boy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2boy__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2boy__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2boy__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	3-CHLOROCATECHOL 1,2-DIOXYGENASE
Molecular weight formula_weight	28131.6 kDa
EC 编号 ec_number	1.13.11.1
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	17938

MSTDRTGNIVGKMIAAINAVIKDEKVSYSEYKASTGWLISVGEKNEWPLFLDVFFEHAIESVAAESNRGSQSSIQGPYFIPGAPELSIPYTMPMRDDESGDTLIFRGEVVDQEGAPLADVLLDMWQADAAGEYSFINPTLPDYLFRGKIRTDENGRFTLRTIVPAPYEIPKNGPTGALLAAAGWHAWRPAHLHWIIAKEGYESLTTQLYFENGQWTGSDVANAVKPELLLSLDKIEAQSGPHFETSYKFTLGKV

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	BENZHYDROXAMIC ACID
Molecular weight formula_weight	137.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
Molecular weight formula_weight	648.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1800

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2boya_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boyb_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boyc_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boyd_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boye_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boyf_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boyg_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

Domain ID domain_id	d2boyh_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2boyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	2boyH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

▶

Unit-cell length a length_a	83.179 Å
Unit-cell length b length_b	86.610 Å
Unit-cell length c length_c	93.447 Å
Unit-cell angle α angle_alpha	85.37 °
Unit-cell angle β angle_beta	66.53 °
Unit-cell angle γ angle_gamma	76.94 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	84.510 Å
R factor r_factor	0.1780
R_work r_work	0.1760
R_free r_free	0.2190

Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP

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

3-CHLOROCATECHOL 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

2boy__assembly_1__model_1

2boy__assembly_1__model_1 | I(q)

2boy__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

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)

Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP

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

3-CHLOROCATECHOL 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

2boy__assembly_1__model_1

2boy__assembly_1__model_1 | I(q)

2boy__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

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)