3e08

H55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase

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

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	TRYPTOPHAN × 8 PROTOPORPHYRIN IX CONTAINING FE × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	TRYPTOPHAN × 8 PROTOPORPHYRIN IX CONTAINING FE × 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 Author chain C； PDBConstruct 1–298； UniProt 1–298 Author chain D； PDBConstruct 1–298； UniProt 1–298 Author chain E； PDBConstruct 1–298； UniProt 1–298 Author chain F； PDBConstruct 1–298； UniProt 1–298 Author chain G； PDBConstruct 1–298； UniProt 1–298 Author chain H； 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	3e08
Deposition date deposition_date	2008-07-31
Structure title title	H55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase
Keywords keywords	TDO, heme, tryptophan 2, 3-dioxygenase, H55S, OXIDOREDUCTASE, Dioxygenase; 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.

3e08__assembly_1__model_1

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

Download this curve (.dat)

3e08__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e08__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.32 Å
Rg (electron density)	28.82 Å
Total Rg	29.66 Å
Atom count	9509
Residues	1120
Excluded volume	168650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e08__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e08__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 (4)

Entity 1 Entity 1 polymer

Description description	Tryptophan 2,3-dioxygenase
Molecular weight formula_weight	34609.2 kDa
EC 编号 ec_number	1.13.11.11
Mutation mutation	H55S
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	20880

MPVDKNLRDLEPGIHTDLEGRLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQSQTSELWLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVLGPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFGHAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRHMRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSVGVDNRPPQGSADAGKR

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	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	16

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	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1955

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3e08a_
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	d3e08b_
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	d3e08c_
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	d3e08d_
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	d3e08e_
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	d3e08f_
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	d3e08g_
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	d3e08h_
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 (8 domains)

Domain ID domain_id	3e08A00
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	3e08B00
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	3e08C00
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	3e08D00
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	3e08E00
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	3e08F00
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	3e08G00
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	3e08H00
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	77.912 Å
Unit-cell length b length_b	117.718 Å
Unit-cell length c length_c	138.978 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.64 °
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	1.900 Å
Low-resolution limit resolution_low	17.560 Å
R factor r_factor	—
R_work r_work	0.1776
R_free r_free	0.2158

H55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase

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

3e08__assembly_1__model_1

3e08__assembly_1__model_1 | I(q)

3e08__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

H55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase

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

3e08__assembly_1__model_1

3e08__assembly_1__model_1 | I(q)

3e08__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)