2nox

Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans

Method: X-RAY DIFFRACTION

▼

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

Tryptophan 2,3-dioxygenase

OrganismNot specified

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 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	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	Q1LK00_RALME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 19–299 Author chain B； PDBConstruct 1–281； UniProt 19–299 Author chain C； PDBConstruct 1–281； UniProt 19–299 Author chain D； PDBConstruct 1–281； UniProt 19–299 Author chain E； PDBConstruct 1–281； UniProt 19–299 Author chain F； PDBConstruct 1–281； UniProt 19–299 Author chain G； PDBConstruct 1–281； UniProt 19–299 Author chain H； PDBConstruct 1–281； UniProt 19–299 Author chain I； PDBConstruct 1–281； UniProt 19–299 Author chain J； PDBConstruct 1–281； UniProt 19–299 Author chain K； PDBConstruct 1–281； UniProt 19–299 Author chain L； PDBConstruct 1–281； UniProt 19–299 Author chain M； PDBConstruct 1–281； UniProt 19–299 Author chain N； PDBConstruct 1–281； UniProt 19–299 Author chain O； PDBConstruct 1–281； UniProt 19–299 Author chain P； PDBConstruct 1–281； UniProt 19–299

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2nox
Deposition date deposition_date	2006-10-26
Structure title title	Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans
Keywords keywords	helical bundle, heme protein, Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2nox__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2nox__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nox__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	29.57 Å
Rg (electron density)	28.21 Å
Total Rg	29.02 Å
Atom count	8674
Residues	1031
Excluded volume	154000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nox__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nox__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nox__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2nox__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tryptophan 2,3-dioxygenase
Molecular weight formula_weight	32542.8 kDa
EC 编号 ec_number	1.13.11.11
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	36423

DGGDSGDTGNGWHGAQMDFARDMSYGDYLGLDQILSAQHPLSPDHNEMLFIVQHQTTELWMKLMLHELRAARDGVKSDQLQPAFKMLARVSRIMDQLVQAWNVLATMTPPEYSAMRPYLGASSGFQSYQYREIEFILGNKNAAMLRPHAHRPEHLELVETALHTPSMYDEAIRLMARRGFQIDPEVVERDWTQPTQYNASVEAAWLEVYRNPSAHWELYELGEKFVDLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRRMLDVVLFPELWKLRTDL

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	16

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1543

▼

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2noxa_
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	d2noxb_
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	d2noxc_
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	d2noxd_
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	d2noxe_
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	d2noxf_
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	d2noxg_
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	d2noxh_
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	d2noxi_
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	d2noxj_
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	d2noxk_
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	d2noxl_
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	d2noxm_
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	d2noxn_
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	d2noxo_
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	d2noxp_
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 (16 domains)

Domain ID domain_id	2noxA00
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	2noxB00
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	2noxC00
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	2noxD00
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	2noxE00
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	2noxF00
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	2noxG00
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	2noxH00
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	2noxI00
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	2noxJ00
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	2noxK00
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	2noxL00
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	2noxM00
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	2noxN00
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	2noxO00
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	2noxP00
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 —

▶

Unit-cell length a length_a	72.544 Å
Unit-cell length b length_b	132.121 Å
Unit-cell length c length_c	139.950 Å
Unit-cell angle α angle_alpha	66.97 °
Unit-cell angle β angle_beta	85.06 °
Unit-cell angle γ angle_gamma	89.89 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	50.120 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2700

Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans

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

2nox__assembly_4__model_1

2nox__assembly_4__model_1 | I(q)

2nox__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans

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

2nox__assembly_4__model_1

2nox__assembly_4__model_1 | I(q)

2nox__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)