SAXSdb — 1dmh

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

CATECHOL 1,2-DIOXYGENASE

Acinetobacter sp.

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 4-METHYLCATECHOL × 2 [1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATA_ACIAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 1–311 Author chain B； PDBConstruct 1–311； UniProt 1–311

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	1dmh
Deposition date deposition_date	1999-12-14
Structure title title	STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL
Keywords keywords	DIOXYGENASE, AROMATIC HYDROCARBON DEGRADATION, ALPHA/BETA FOLD, METALLOENZYME, SUBSTRATE, 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.

1dmh__assembly_1__model_1

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

Download this curve (.dat)

1dmh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dmh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.67 Å
Rg (electron density)	30.05 Å
Total Rg	30.48 Å
Atom count	4920
Residues	618
Excluded volume	86687 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dmh__assembly_1__model_1`	dimeric （2）	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	CATECHOL 1,2-DIOXYGENASE
Molecular weight formula_weight	34384.1 kDa
EC 编号 ec_number	1.13.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5190

MEVKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVAYLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVDNQVVDRPRLAV

Source Source

Source organism organism	Acinetobacter sp.
NCBI taxonomy ID ncbi_taxonomy_id	62977
Host organism host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	4-METHYLCATECHOL
Molecular weight formula_weight	124.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE
Molecular weight formula_weight	636.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dmha_
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.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d1dmhb_
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.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (2 domains)

Domain ID domain_id	1dmhA00
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	1dmhB00
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

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Unit-cell length a length_a	52.800 Å
Unit-cell length b length_b	88.000 Å
Unit-cell length c length_c	84.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2180

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL

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

CATECHOL 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

1dmh__assembly_1__model_1

1dmh__assembly_1__model_1 | I(q)

1dmh__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)

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL

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

CATECHOL 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

1dmh__assembly_1__model_1

1dmh__assembly_1__model_1 | I(q)

1dmh__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)