6dz4

Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site

Method: X-RAY DIFFRACTION Dmax: 97.4 Å Quality: GOOD

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–268 Not recorded Tryptophan synthase beta chain × 2 (P0A2K1) CL CHLORIDE ION × 16 DMS DIMETHYL SULFOXIDE × 24 KOU (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine × 2 NA SODIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;297 K;50mM Bicine-NaOH, pH 7.8, containing 9% PEG3350, 50mM NaCl, 2mM spermine Resolution 1.45 Å R-free 0.186

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–397 Not recorded Tryptophan synthase alpha chain × 2 (P00929) CL CHLORIDE ION × 16 DMS DIMETHYL SULFOXIDE × 24 KOU (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine × 2 NA SODIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;297 K;50mM Bicine-NaOH, pH 7.8, containing 9% PEG3350, 50mM NaCl, 2mM spermine Resolution 1.45 Å R-free 0.186

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 6dz4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dz4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dz4
Deposition date deposition_date2018-07-02
Structure title titleCrystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site
Keywords keywordsF9F, 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_guinier27.53
Radius of gyration Rg (electron density) rg_electron26.69
Forward intensity I(0) i084465100.00
Molecular weight molecular_weight71619.0 kDa
Excluded volume excluded_volume89377 ų
Envelope volume envelope_volume103310 ų
Hydration-shell volume shell_volume32453 ų
Envelope diameter envelope_diameter95.7
Shell Rg shell_rg34.01
Envelope Rg envelope_rg26.96
Shape Rg shape_rg26.65
Total Rg total_rg27.54
Total atoms total_atoms5002
Residues n_residues650
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 dmax97.4
Rg (real space) rg_real27.60
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real8.4470e+07
I(0) uncertainty (real space) i0_real_error1.1980e+06
Rg (reciprocal space) rg_reciprocal27.58
I(0) (reciprocal space) i0_reciprocal84460000.0000
Solution quality estimate total_estimate0.8519
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.2
Skewness Skewness skewness0.453
Kurtosis Kurtosis kurtosis-0.251
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24430000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6dz4a_
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_idd6dz4b_
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_id6dz4A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id6dz4B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1100
Domain ID domain_id6dz4B02
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)