3bgx

E. coli Thymidylate Synthase C146S mutant complexed with dTMP and MTF

Method: X-RAY DIFFRACTION Dmax: 59.9 Å Quality: GOOD

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

Thymidylate synthase

Escherichia coli

UniProt P0A884

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–264 Mutation:C146S Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 TMP THYMIDINE-5'-PHOSPHATE × 2 MEF N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;2.5 M ammonium sulfate, 20 mM KH2PO4, 4MM DTT, 4MM dTMP, 4MM methylene tetrahydrofolate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.93 Å R-free 0.230

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.

56 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TYSY_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–264; UniProt 1–264

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 3bgx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3bgx
Deposition date deposition_date2007-11-27
Structure title titleE. coli Thymidylate Synthase C146S mutant complexed with dTMP and MTF
Keywords keywordsmethyltransferase, Nucleotide biosynthesis, Repressor, RNA-binding, Translation regulation, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.62
Radius of gyration Rg (electron density) rg_electron18.11
Forward intensity I(0) i017861100.00
Molecular weight molecular_weight31470.0 kDa
Excluded volume excluded_volume39075 ų
Envelope volume envelope_volume44964 ų
Hydration-shell volume shell_volume20291 ų
Envelope diameter envelope_diameter59.2
Shell Rg shell_rg24.96
Envelope Rg envelope_rg18.40
Shape Rg shape_rg18.09
Total Rg total_rg19.11
Total atoms total_atoms2217
Residues n_residues263
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 dmax59.9
Rg (real space) rg_real19.46
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real1.7860e+07
I(0) uncertainty (real space) i0_real_error1.7800e+05
Rg (reciprocal space) rg_reciprocal19.48
I(0) (reciprocal space) i0_reciprocal17860000.0000
Solution quality estimate total_estimate0.7699
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.2
Skewness Skewness skewness0.087
Kurtosis Kurtosis kurtosis-0.470
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3707000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.987; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3bgxa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamilyd.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family familyd.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (1 domains)

Domain ID domain_id3bgxA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain

8. Citations (1)

9. Files and Curves (10)