7ly8

The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring

Method: X-RAY DIFFRACTION Dmax: 93.8 Å Quality: REASONABLE

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

Tryptophan synthase alpha chain

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt P00929

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–268 Not recorded Tryptophan synthase beta chain × 1 (P0A2K1) F6F 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE × 3 CL CHLORIDE ION × 5 PLP PYRIDOXAL-5'-PHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;298 K;50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8 Resolution 1.55 Å R-free 0.194

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.

112 other PDB entries and 115 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPA_SALTY
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–268; UniProt 1–268

Tryptophan synthase beta chain

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt P0A2K1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–397 Not recorded Tryptophan synthase alpha chain × 1 (P00929) F6F 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE × 3 CL CHLORIDE ION × 5 PLP PYRIDOXAL-5'-PHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;298 K;50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8 Resolution 1.55 Å R-free 0.194

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.

119 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPB_SALTY
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–397; UniProt 1–397

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 7ly8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ly8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ly8
Deposition date deposition_date2021-03-06
Structure title titleThe internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
Keywords keywordsinhibitor, internal aldimine, LYASE, LYASE-LYASE INHIBITOR complex; LYASE/LYASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.39
Radius of gyration Rg (electron density) rg_electron26.60
Forward intensity I(0) i082733600.00
Molecular weight molecular_weight70728.0 kDa
Excluded volume excluded_volume88106 ų
Envelope volume envelope_volume101600 ų
Hydration-shell volume shell_volume32074 ų
Envelope diameter envelope_diameter95.9
Shell Rg shell_rg33.93
Envelope Rg envelope_rg26.90
Shape Rg shape_rg26.57
Total Rg total_rg27.39
Total atoms total_atoms4955
Residues n_residues645
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax93.8
Rg (real space) rg_real27.48
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real8.2730e+07
I(0) uncertainty (real space) i0_real_error1.2000e+06
Rg (reciprocal space) rg_reciprocal27.46
I(0) (reciprocal space) i0_reciprocal82730000.0000
Solution quality estimate total_estimate0.6615
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.476
Kurtosis Kurtosis kurtosis-0.221
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27610000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 0.127; Positv: 1.000; Valcen: 0.970; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)