SAXSdb — 1yw0

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

tryptophan 2,3-dioxygenase

Xanthomonas campestris pv. campestris str. ATCC 33913

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PDA8_XANCP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 23–298 Author chain B； PDBConstruct 1–276； UniProt 23–298 Author chain C； PDBConstruct 1–276； UniProt 23–298 Author chain D； PDBConstruct 1–276； UniProt 23–298

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	1yw0
Deposition date deposition_date	2005-02-16
Structure title title	Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.
Keywords keywords	;tryptophan, dioxygenase, NESG, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, 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.

1yw0__assembly_1__model_1

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

Download this curve (.dat)

1yw0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yw0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.95 Å
Rg (electron density)	28.63 Å
Total Rg	29.40 Å
Atom count	8169
Residues	951
Excluded volume	145560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yw0__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 (3)

Entity 1 Entity 1 polymer

Description description	tryptophan 2,3-dioxygenase
Molecular weight formula_weight	32389.9 kDa
EC 编号 ec_number	1.13.11.11
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	8274

TYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGVDNRPPQGSADAGKR

Source Source

Source organism organism	Xanthomonas campestris pv. campestris str. ATCC 33913
NCBI taxonomy ID ncbi_taxonomy_id	190485
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yw0a1
Class class	a — All alpha proteins
Fold Fold fold	a.266 — Indolic compounds 2,3-dioxygenase-like
Superfamily Superfamily superfamily	a.266.1 — Indolic compounds 2,3-dioxygenase-like
Family Family family	a.266.1.1 — Bacterial tryptophan 2,3-dioxygenase

Domain ID domain_id	d1yw0b_
Class class	a — All alpha proteins
Fold Fold fold	a.266 — Indolic compounds 2,3-dioxygenase-like
Superfamily Superfamily superfamily	a.266.1 — Indolic compounds 2,3-dioxygenase-like
Family Family family	a.266.1.1 — Bacterial tryptophan 2,3-dioxygenase

Domain ID domain_id	d1yw0c_
Class class	a — All alpha proteins
Fold Fold fold	a.266 — Indolic compounds 2,3-dioxygenase-like
Superfamily Superfamily superfamily	a.266.1 — Indolic compounds 2,3-dioxygenase-like
Family Family family	a.266.1.1 — Bacterial tryptophan 2,3-dioxygenase

Domain ID domain_id	d1yw0d_
Class class	a — All alpha proteins
Fold Fold fold	a.266 — Indolic compounds 2,3-dioxygenase-like
Superfamily Superfamily superfamily	a.266.1 — Indolic compounds 2,3-dioxygenase-like
Family Family family	a.266.1.1 — Bacterial tryptophan 2,3-dioxygenase

CATH v4.4 (4 domains)

Domain ID domain_id	1yw0A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	480 —

Domain ID domain_id	1yw0B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	480 —

Domain ID domain_id	1yw0C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	480 —

Domain ID domain_id	1yw0D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	480 —

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Unit-cell length a length_a	89.701 Å
Unit-cell length b length_b	110.223 Å
Unit-cell length c length_c	149.398 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	29.320 Å
R factor r_factor	0.2500
R_work r_work	0.2500
R_free r_free	0.2940

Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.

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

tryptophan 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

1yw0__assembly_1__model_1

1yw0__assembly_1__model_1 | I(q)

1yw0__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.

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

tryptophan 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

1yw0__assembly_1__model_1

1yw0__assembly_1__model_1 | I(q)

1yw0__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)