3cep

Structure of a tryptophan synthase quinonoid intermediate

Method: X-RAY DIFFRACTION Dmax: 91.6 Å Quality: GOOD

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

Tryptophan synthase alpha chain

Salmonella 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) G3P SN-GLYCEROL-3-PHOSPHATE × 2 IDM INDOLINE × 4 CS CESIUM ION × 6 PLP PYRIDOXAL-5'-PHOSPHATE × 2 MH6 3-hydroxy-2-iminopropanoic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;50mM bicine (pH 7.8), 1mM EDTA, 5mM dithioerythritol, 0.02mM pyridoxal phosphate solution, 2mM spermine, and 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.238

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

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 2–397 Not recorded Tryptophan synthase alpha chain × 2 (P00929) G3P SN-GLYCEROL-3-PHOSPHATE × 2 IDM INDOLINE × 4 CS CESIUM ION × 6 PLP PYRIDOXAL-5'-PHOSPHATE × 2 MH6 3-hydroxy-2-iminopropanoic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;50mM bicine (pH 7.8), 1mM EDTA, 5mM dithioerythritol, 0.02mM pyridoxal phosphate solution, 2mM spermine, and 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.238

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 1–396; UniProt 2–397

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 3cep

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cep
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cep
Deposition date deposition_date2008-02-29
Structure title titleStructure of a tryptophan synthase quinonoid intermediate
Keywords keywords;LYASE, CARBON-OXYGEN LYASE, TRYPTOPHAN BIOSYNTHESIS, Allosteric enzyme, Amino-acid biosynthesis, Aromatic amino acid biosynthesis, Pyridoxal phosphate ;; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.01
Radius of gyration Rg (electron density) rg_electron26.22
Forward intensity I(0) i082506800.00
Molecular weight molecular_weight71329.0 kDa
Excluded volume excluded_volume89072 ų
Envelope volume envelope_volume100840 ų
Hydration-shell volume shell_volume32098 ų
Envelope diameter envelope_diameter92.9
Shell Rg shell_rg33.77
Envelope Rg envelope_rg26.51
Shape Rg shape_rg26.18
Total Rg total_rg27.06
Total atoms total_atoms4988
Residues n_residues659
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 dmax91.6
Rg (real space) rg_real27.07
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real8.2510e+07
I(0) uncertainty (real space) i0_real_error1.1340e+06
Rg (reciprocal space) rg_reciprocal27.05
I(0) (reciprocal space) i0_reciprocal82510000.0000
Solution quality estimate total_estimate0.8613
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5
Skewness Skewness skewness0.448
Kurtosis Kurtosis kurtosis-0.254
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25890000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.908

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cepa_
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_idd3cepb_
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_id3cepA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id3cepB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1100
Domain ID domain_id3cepB02
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)