6c73

Tryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site

Method: X-RAY DIFFRACTION Dmax: 74.9 Å Quality: REASONABLE

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

Tryptophan synthase alpha chain

Salmonella enterica subsp. enterica serovar Typhimurium

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–268 Not recorded Tryptophan synthase beta chain × 2 (P0A2K1) DMS DIMETHYL SULFOXIDE × 40 F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 10 CS CESIUM ION × 8 PLP PYRIDOXAL-5'-PHOSPHATE × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;298 K;100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 1 mM DTT, 1 mM EDTA, 2 mM F9F Resolution 1.65 Å R-free 0.183

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 enterica subsp. enterica serovar Typhimurium

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–396 Mutation:Q114A Tryptophan synthase alpha chain × 2 (P00929) DMS DIMETHYL SULFOXIDE × 40 F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 10 CS CESIUM ION × 8 PLP PYRIDOXAL-5'-PHOSPHATE × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;298 K;100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 1 mM DTT, 1 mM EDTA, 2 mM F9F Resolution 1.65 Å R-free 0.183

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 1–395; UniProt 2–396

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 6c73

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c73
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c73
Deposition date deposition_date2018-01-19
Structure title titleTryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site
Keywords keywordsF9F ligand, cesium ion, mutant beta-Q114A, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.49
Radius of gyration Rg (electron density) rg_electron26.69
Forward intensity I(0) i090276500.00
Molecular weight molecular_weight74215.0 kDa
Excluded volume excluded_volume92542 ų
Envelope volume envelope_volume106930 ų
Hydration-shell volume shell_volume33359 ų
Envelope diameter envelope_diameter97.2
Shell Rg shell_rg34.30
Envelope Rg envelope_rg27.04
Shape Rg shape_rg26.64
Total Rg total_rg27.61
Total atoms total_atoms5153
Residues n_residues663
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 dmax74.9
Rg (real space) rg_real26.46
Rg uncertainty (real space) rg_real_error0.13
I(0) (real space) i0_real8.6570e+07
I(0) uncertainty (real space) i0_real_error9.4820e+05
Rg (reciprocal space) rg_reciprocal27.53
I(0) (reciprocal space) i0_reciprocal90280000.0000
Solution quality estimate total_estimate0.6814
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.7
Skewness Skewness skewness0.361
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha2.1960
Highest regularization parameter α highest_alpha24720000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.971; Stabil: 0.982; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6c73a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.4 — Tryptophan biosynthesis enzymes
Domain ID domain_idd6c73b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamilyc.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family familyc.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

CATH v4.4 (3 domains)

Domain ID domain_id6c73A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id6c73B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1100
Domain ID domain_id6c73B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1100

8. Citations (1)

9. Files and Curves (10)