9dy7

Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine and Na+

Method: X-RAY DIFFRACTION

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

Tryptophanase (with internal aldimine)

Proteus vulgaris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	DIMETHYL SULFOXIDE × 4 1,2-ETHANEDIOL × 2 2-AMINO-4-ETHYL SULFANYL BUTYRIC ACID × 2 SODIUM ION × 4 (2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid × 1 (E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNAA_PROVU
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–466； UniProt 2–467 Author chain C； PDBConstruct 1–466； UniProt 2–467 Author chain B； PDBConstruct 1–466； UniProt 2–467 Author chain D； PDBConstruct 1–466； UniProt 2–467

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	9dy7
Deposition date deposition_date	2024-10-13
Last revision last_revision	2025-04-16
Structure title title	Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine and Na+
Keywords keywords	;pyridoxal-5'-phosphate, aminotransferase fold, cation activation, inhibitor complex, LYASE ;; LYASE
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.

9dy7__assembly_1__model_1

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

Download this curve (.dat)

9dy7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dy7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.09 Å
Rg (electron density)	36.48 Å
Total Rg	36.94 Å
Atom count	14855
Residues	1862
Excluded volume	265370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dy7__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 (9)

Entity 1 Entity 1 polymer

Description description	Tryptophanase (with internal aldimine)
Molecular weight formula_weight	52655.9 kDa
EC 编号 ec_number	4.1.99.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	16300

AKRIVEPFRIKMVEKIRVPSREEREAALKEAGYNPFLLPSSAVYIDLLTDSGTNAMSDHQWAAMITGDEAYAGSRNYYDLKDKAKELFNYDYIIPAHQGRGAENILFPVLLKYKQKEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSETYDDWKGDFDIKKLKENIAQHGADNIVAIVSTVTCNSAGGQPVSMSNLKEVYEIAKQHGIFVVMDSARFCENAYFIKARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVAIRDNEEIFTLARQRCVPMEGFVTYGGLAGRDMAAMVQGLEEGTEEEYLHYRIGQVKYLGDRLREAGIPIQYPTGGHAVFVDCKKLVPQIPGDQFPAQAVINALYLESGVRAVEIGSFLLGRDPATGEQKHADMEFMRLTIARRVYTNDHMDYIADALIGLKEKFATLKGLEFEYEPPVLRHFTARLKPIE

Source Source

Source organism organism	Proteus vulgaris
NCBI taxonomy ID ncbi_taxonomy_id	585
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Tryptophanase
Molecular weight formula_weight	52427.8 kDa
EC 编号 ec_number	4.1.99.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

Source Source

Source organism organism	Proteus vulgaris
NCBI taxonomy ID ncbi_taxonomy_id	585
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-4-ETHYL SULFANYL BUTYRIC ACID
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	(2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid
Molecular weight formula_weight	392.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	(E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine
Molecular weight formula_weight	392.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1210

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Unit-cell length a length_a	111.330 Å
Unit-cell length b length_b	113.676 Å
Unit-cell length c length_c	149.414 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	52.160 Å
R factor r_factor	0.1561
R_work r_work	0.1557
R_free r_free	0.1854

Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine and Na+

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

Tryptophanase (with internal aldimine)

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

9dy7__assembly_1__model_1

9dy7__assembly_1__model_1 | I(q)

9dy7__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine and Na+

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

Tryptophanase (with internal aldimine)

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

9dy7__assembly_1__model_1

9dy7__assembly_1__model_1 | I(q)

9dy7__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)