SAXSdb — 2ei0

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

1,2-dihydroxynaphthalene dioxygenase

Pseudomonas sp.

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 MAGNESIUM ION × 8 1,1'-BIPHENYL-3,4-DIOL × 24 GLYCEROL × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAHC_PSEU8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 1–302

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	2ei0
Deposition date deposition_date	2007-03-10
Structure title title	Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl
Keywords keywords	extradiol dioxygenase, protein substrate complex, 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.

2ei0__assembly_1__model_1

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

Download this curve (.dat)

2ei0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ei0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.63 Å
Rg (electron density)	39.71 Å
Total Rg	40.28 Å
Atom count	18592
Residues	2288
Excluded volume	329010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ei0__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 (6)

Entity 1 Entity 1 polymer

Description description	1,2-dihydroxynaphthalene dioxygenase
Molecular weight formula_weight	33985.6 kDa
EC 编号 ec_number	1.13.11.-
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	2673

MSKQAAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIPLPNGMTAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGYGLDVKLS

Source Source

Source organism organism	Pseudomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	69011
Host organism host_organism	Pseudomonas putida

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,1'-BIPHENYL-3,4-DIOL
Molecular weight formula_weight	186.2 kDa
Source method src_method	syn
Copy count entity_count	3

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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ei0a1
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.32.1.0 — automated matches

Domain ID domain_id	d2ei0a2
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.32.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2ei0A01
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	2ei0A02
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	117.870 Å
Unit-cell length b length_b	117.870 Å
Unit-cell length c length_c	121.594 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	1.600 Å
Low-resolution limit resolution_low	49.150 Å
R factor r_factor	0.1606
R_work r_work	0.1598
R_free r_free	0.1756

Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl

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

1,2-dihydroxynaphthalene 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

2ei0__assembly_1__model_1

2ei0__assembly_1__model_1 | I(q)

2ei0__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 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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl

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

1,2-dihydroxynaphthalene 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

2ei0__assembly_1__model_1

2ei0__assembly_1__model_1 | I(q)

2ei0__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 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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)