7p46

Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)

Method: X-RAY DIFFRACTION

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

Tryptophan 2,3-dioxygenase

Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 CYANIDE ION × 4 (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid × 4 TRYPTOPHAN × 4 GLYCEROL × 10 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 CYANIDE ION × 2 (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid × 4 TRYPTOPHAN × 4 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T23O_XANCP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–282； UniProt 5–286 Author chain B； PDBConstruct 1–282； UniProt 5–286 Author chain C； PDBConstruct 1–282； UniProt 5–286 Author chain D； PDBConstruct 1–282； UniProt 5–286 Author chain E； PDBConstruct 1–282； UniProt 5–286 Author chain F； PDBConstruct 1–282； UniProt 5–286 Author chain G； PDBConstruct 1–282； UniProt 5–286 Author chain H； PDBConstruct 1–282； UniProt 5–286

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	7p46
Deposition date deposition_date	2021-07-09
Structure title title	Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)
Keywords keywords	dioxygenase, cyanide, kynurenine, 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.

7p46__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7p46__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7p46__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.17 Å
Rg (electron density)	28.70 Å
Total Rg	29.52 Å
Atom count	9498
Residues	1114
Excluded volume	168440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7p46__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7p46__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Tryptophan 2,3-dioxygenase
Molecular weight formula_weight	32942.3 kDa
EC 编号 ec_number	1.13.11.11
Source method src_method	man
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	21574

KNLRDLEPGIHTDLEGRLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQSQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGVDN

Source Source

Source organism organism	Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
NCBI taxonomy ID ncbi_taxonomy_id	190485
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid
Molecular weight formula_weight	208.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1924

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Unit-cell length a length_a	78.095 Å
Unit-cell length b length_b	117.752 Å
Unit-cell length c length_c	138.819 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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	89.780 Å
R factor r_factor	0.1507
R_work r_work	0.1488
R_free r_free	0.1851

Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)

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

7p46__assembly_2__model_1

7p46__assembly_2__model_1 | I(q)

7p46__assembly_2__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 (7)

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 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)

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

7p46__assembly_2__model_1

7p46__assembly_2__model_1 | I(q)

7p46__assembly_2__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 (7)

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 non-polymer

Entity 7 Entity 7 water

7. Citations (1)