SAXSdb — 3eby

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

beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase

Novosphingobium aromaticivorans DSM 12444

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	CHLORIDE ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4XDU4_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–163； UniProt 1–162

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	3eby
Deposition date deposition_date	2008-08-28
Structure title title	Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution
Keywords keywords	;YP_001165631.1, the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Dioxygenase, Unknown function ;; structural genomics, unknown function
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.

3eby__assembly_1__model_1

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

Download this curve (.dat)

3eby__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eby__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.77 Å
Rg (electron density)	21.69 Å
Total Rg	22.79 Å
Atom count	3513
Residues	453
Excluded volume	62369 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eby__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase
Molecular weight formula_weight	18114.0 kDa
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	1412

GMSVAAEVAQVAQSAIDDFNAAYGLCLDDDRLEQWPTLFVDDCLYQVIARENVDNGLPAAVMYCDSKGMLADRVVALRKANVFPEHFNRHLIGRAVITGVEGDQVSAEASYVVFQTRNDGETRIYNAGKYVDRFDLSGGTVRLKSRTCIYDTLRIATLLATPI

Source Source

Source organism organism	Novosphingobium aromaticivorans DSM 12444
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ebya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.4 — Ring hydroxylating beta subunit

CATH v4.4 (1 domains)

Domain ID domain_id	3ebyA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	80.290 Å
Unit-cell length b length_b	80.290 Å
Unit-cell length c length_c	145.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	26.764 Å
R factor r_factor	0.1700
R_work r_work	0.1680
R_free r_free	0.2050

Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution

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

beta subunit of a putative Aromatic-ring-hydroxylating 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

3eby__assembly_1__model_1

3eby__assembly_1__model_1 | I(q)

3eby__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution

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

beta subunit of a putative Aromatic-ring-hydroxylating 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

3eby__assembly_1__model_1

3eby__assembly_1__model_1 | I(q)

3eby__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)