9dy7

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

Method: X-RAY DIFFRACTION D_max: 109.5 Å Quality: GOOD

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–467 Chain B； UniProt 2–467 Chain C； UniProt 2–467 Chain D； UniProt 2–467	Non-standard monomer：Yes (specific site not provided by mmCIF)	DMS DIMETHYL SULFOXIDE × 4 EDO 1,2-ETHANEDIOL × 2 ESC 2-AMINO-4-ETHYL SULFANYL BUTYRIC ACID × 2 NA SODIUM ION × 4 YAR (2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid × 1 YAE (E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 0.2 M KCl, 22% PEG 4000	Resolution 1.87 Å R-free 0.185

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9DY7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AX4 TRYPTOPHANASE FROM PROTEUS VULGARIS Deposited 1997-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；27 % PEG 4000, 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.8, 0.25 MM PYRIDOXAL 5'-PHOSPHATE, 5MM DTT, 0.1 M CSCL.	Resolution 2.10 Å R-free 0.227
5W19 Tryptophan indole-lyase complex with oxindolyl-L-alanine Deposited 2017-06-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 4 9TD 1-carboxy-1-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]azaniumyl}-2-[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-ide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；35 mM potassium phosphate, 0.05 M HEPES, 0.3 M KCl, 11% PEG 4000	Resolution 2.10 Å R-free 0.244
5W1B Tryptophan indole-lyase Deposited 2017-06-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；35 mM potassium phosphate, 0.05 M HEPES, 0.3 M KCl, 11% PEG 4000	Resolution 2.00 Å R-free 0.252
8V2K Proteus vulgaris tryptophan indole-lyase complexed with L-alanine Deposited 2023-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 4 F0G (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine × 2 DMS DIMETHYL SULFOXIDE × 2 PLI (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.1 M potassium phosphate, pH 8.0, 0.1 mM pyrodoxal-5'-phosphate, 1 mM DTT, 0.2 M CsCl, 22% PEG 4000	Resolution 1.81 Å R-free 0.231
8V4A Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine Deposited 2023-11-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 4 YAE (E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine × 2 YAR (2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M Potassium phosphate, pH 8.0, 0.1 mM PLP, 1 mM DTT, 0.2 M CsCl, 22% PEG 4000	Resolution 1.96 Å R-free 0.224
8V6P Proteus vulgaris tryptophan indole-lyase complexed with 7-aza-L-tryptophan Deposited 2023-12-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 2 A1ACN (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-(1H-pyrrolo[2,3-b]pyridin-3-yl)-L-alanine × 2 DMS DIMETHYL SULFOXIDE × 1 A1ABZ (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-(1H-pyrrolo[2,3-b]pyridin-3-yl)propanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 0.2 M CsCl, 22% PEG 4000	Resolution 1.74 Å R-free 0.228
8V9P Proteus vulgaris tryptophan indole-lyase complexed with (3S)-dioxindolyl-L-alanine Deposited 2023-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 4 YQK (2~{E})-2-[(~{Z})-[2-methyl-3-oxidanyl-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-1~{H}-pyridin-4-ylidene]methyl]imino-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-1~{H}-indol-3-yl]propanoic acid × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 22% PEG 4000, 0.2 M CsCl	Resolution 1.85 Å R-free 0.247
9BLV Proteus vulgaris tryptophan indole-lyase complexed with L-Trp and benzimidazole Deposited 2024-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 4 BZI BENZIMIDAZOLE × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 DMS DIMETHYL SULFOXIDE × 2 PLT [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-L-TRYPTOPHANE × 1 A1A2Z N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tryptophan × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M potassium phosphate, pH 8, 0.2 M CsCl, 22% PEG 4000	Resolution 1.78 Å R-free 0.247
9BNJ Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole Deposited 2024-05-02	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–467（467 aa） Chain B 1–467（467 aa） Chain C 1–467（467 aa） Chain D 1–467（467 aa）	Not recorded	K POTASSIUM ION × 4 BZI BENZIMIDAZOLE × 5 DMS DIMETHYL SULFOXIDE × 1 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 0.2 M KCl, 22% PEG 4000	Resolution 1.51 Å R-free 0.180

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dy7
Deposition date deposition_date	2024-10-13
最后修订 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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.09 Å
Radius of gyration Rg (electron density) rg_electron	36.48 Å
Forward intensity I(0) i0	644616000.00
Molecular weight molecular_weight	211110.0 kDa
Excluded volume excluded_volume	265370 Å³
Envelope volume envelope_volume	311830 Å³
Hydration-shell volume shell_volume	66480 Å³
Envelope diameter envelope_diameter	116.1 Å
Shell Rg shell_rg	45.92 Å
Envelope Rg envelope_rg	36.76 Å
Shape Rg shape_rg	36.49 Å
Total Rg total_rg	36.94 Å
Total atoms total_atoms	14855
Residues n_residues	1862
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.5 Å
Rg (real space) rg_real	36.90 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	6.4460e+08
I(0) uncertainty (real space) i0_real_error	9.8930e+06
Rg (reciprocal space) rg_reciprocal	37.02 Å
I(0) (reciprocal space) i0_reciprocal	644700000.0000
Solution quality estimate total_estimate	0.8732
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.8 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.533
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	255200000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.431

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Proteus vulgaris
NCBI Class编号 ncbi_taxonomy_id	585
宿主生物 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

来源 Source

来源生物 organism	Proteus vulgaris
NCBI Class编号 ncbi_taxonomy_id	585
宿主生物 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/dy/9dy7/9dy7.fit
pddf	/app/data/pr_computation/dy/9dy7/9dy7.pr.out
profile	/app/data/saxs_computation/dy/9dy7/9dy7.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)