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5w1b

Tryptophan indole-lyase

Method: X-RAY DIFFRACTION Dmax: 117.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tryptophanase

Proteus vulgaris

UniProt P28796

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 1–467 Chain B； UniProt 1–467 Chain C； UniProt 1–467 Chain D； UniProt 1–467 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

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 5W1B 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 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 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 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
8V2K Proteus vulgaris tryptophan indole-lyase complexed with L-alanine Deposited 2023-11-22 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 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 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 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 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 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 × 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
9DY7 Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine and Na+ Deposited 2024-10-13 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 2–467（466 aa）
Chain B 2–467（466 aa）
Chain C 2–467（466 aa）
Chain D 2–467（466 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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

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
Chains and sequence ranges Author chain A； PDBConstruct 1–467； UniProt 1–467 Author chain B； PDBConstruct 1–467； UniProt 1–467 Author chain C； PDBConstruct 1–467； UniProt 1–467 Author chain D； PDBConstruct 1–467； UniProt 1–467

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

SAXS profile for 5w1b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5w1b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5w1b
Deposition date deposition_date2017-06-02
Structure title titleTryptophan indole-lyase
Keywords keywords;pyridoxal-5'-phosphate, aminotransferase fold, tryptophan metabolism, LYASE ;; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.22 Å
Radius of gyration Rg (electron density) rg_electron36.60 Å
Forward intensity I(0) i0639616000.00
Molecular weight molecular_weight210480.0 kDa
Excluded volume excluded_volume264600 ų
Envelope volume envelope_volume312560 ų
Hydration-shell volume shell_volume66464 ų
Envelope diameter envelope_diameter116.0 Å
Shell Rg shell_rg46.06 Å
Envelope Rg envelope_rg36.86 Å
Shape Rg shape_rg36.62 Å
Total Rg total_rg37.05 Å
Total atoms total_atoms14816
Residues n_residues1860
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax117.2 Å
Rg (real space) rg_real37.03 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real6.3960e+08
I(0) uncertainty (real space) i0_real_error1.0580e+07
Rg (reciprocal space) rg_reciprocal37.15 Å
I(0) (reciprocal space) i0_reciprocal639700000.0000
Solution quality estimate total_estimate0.8994
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.6 Å
Skewness Skewness skewness0.176
Kurtosis Kurtosis kurtosis-0.537
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha249600000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.937
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5w1ba_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.2 — Beta-eliminating lyases
Domain ID domain_idd5w1bb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.2 — Beta-eliminating lyases
Domain ID domain_idd5w1bc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.2 — Beta-eliminating lyases
Domain ID domain_idd5w1bd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.2 — Beta-eliminating lyases
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8. Citations (1)

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9. Files and Curves (10)