SAXSdb — 2nw9

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

Tryptophan 2,3-dioxygenase

Xanthomonas campestris pv. campestris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	6-FLUORO-L-TRYPTOPHAN × 2 PROTOPORPHYRIN IX CONTAINING FE × 4 MANGANESE (II) ION × 4 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 1–298； UniProt 1–298 Author chain B； PDBConstruct 1–298； UniProt 1–298

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	2nw9
Deposition date deposition_date	2006-11-14
Structure title title	Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and 6-fluoro-tryptophan. Northeast Structural Genomics Target XcR13
Keywords keywords	;all alpha-helical protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

2nw9__assembly_1__model_1

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

Download this curve (.dat)

2nw9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nw9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.05 Å
Rg (electron density)	28.58 Å
Total Rg	29.46 Å
Atom count	9056
Residues	1068
Excluded volume	160790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nw9__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 (5)

Entity 1 Entity 1 polymer

Description description	Tryptophan 2,3-dioxygenase
Molecular weight formula_weight	35731.4 kDa
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	5124

MPVDKNLRDLEPGIHTDLEGRLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGVDNRPPQGSADAGKRLEHHHHHH

Source Source

Source organism organism	Xanthomonas campestris pv. campestris
NCBI taxonomy ID ncbi_taxonomy_id	340
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	6-FLUORO-L-TRYPTOPHAN
Molecular weight formula_weight	222.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	596

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2nw9a_
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.266.1.0 — automated matches

Domain ID domain_id	d2nw9b_
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.266.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2nw9A00
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	2nw9B00
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	114.212 Å
Unit-cell length b length_b	114.212 Å
Unit-cell length c length_c	96.095 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	26.380 Å
R factor r_factor	0.1660
R_work r_work	0.1660
R_free r_free	0.1840

Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and 6-fluoro-tryptophan. 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

2nw9__assembly_1__model_1

2nw9__assembly_1__model_1 | I(q)

2nw9__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 (1)

Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and 6-fluoro-tryptophan. 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

2nw9__assembly_1__model_1

2nw9__assembly_1__model_1 | I(q)

2nw9__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 (1)