2a9w

E. coli TS complexed with dUMP and inhibitor GA9

Method: X-RAY DIFFRACTION Dmax: 130.8 Å Quality: REASONABLE

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 Chain B; UniProt 1–264 Non-standard monomer:Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 6 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 GA9 3,3-BIS(3-BROMO-4-HYDROXYPHENYL)-7-CHLORO-1H,3H-BENZO[DE]ISOCHROMEN-1-ONE × 2 BME BETA-MERCAPTOETHANOL × 2 GOL GLYCEROL × 6 2BR 2-BROMOPHENOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;potassium phosphate, DTT, EDTA, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293 K Resolution 1.65 Å R-free 0.226
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–264 Chain D; UniProt 1–264 Non-standard monomer:Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 6 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 GA9 3,3-BIS(3-BROMO-4-HYDROXYPHENYL)-7-CHLORO-1H,3H-BENZO[DE]ISOCHROMEN-1-ONE × 2 BME BETA-MERCAPTOETHANOL × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;potassium phosphate, DTT, EDTA, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293 K Resolution 1.65 Å R-free 0.226

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 62 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 Author chain B; PDBConstruct 1–264; UniProt 1–264 Author chain C; PDBConstruct 1–264; UniProt 1–264 Author chain D; 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 2a9w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2a9w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2a9w
Deposition date deposition_date2005-07-12
Structure title titleE. coli TS complexed with dUMP and inhibitor GA9
Keywords keywordsprotein-inhibitor complex, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier40.58
Radius of gyration Rg (electron density) rg_electron40.72
Forward intensity I(0) i0252775000.00
Molecular weight molecular_weight126850.0 kDa
Excluded volume excluded_volume157020 ų
Envelope volume envelope_volume197530 ų
Hydration-shell volume shell_volume43201 ų
Envelope diameter envelope_diameter136.9
Shell Rg shell_rg42.33
Envelope Rg envelope_rg40.62
Shape Rg shape_rg40.70
Total Rg total_rg40.87
Total atoms total_atoms8880
Residues n_residues1052
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 dmax130.8
Rg (real space) rg_real40.99
Rg uncertainty (real space) rg_real_error1.10
I(0) (real space) i0_real2.5280e+08
I(0) uncertainty (real space) i0_real_error4.5830e+06
Rg (reciprocal space) rg_reciprocal40.59
I(0) (reciprocal space) i0_reciprocal252700000.0000
Solution quality estimate total_estimate0.7468
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.568
Kurtosis Kurtosis kurtosis-0.490
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha86770000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.666; Smooth: 0.113

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2a9wa_
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
Domain ID domain_idd2a9wb_
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
Domain ID domain_idd2a9wc_
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
Domain ID domain_idd2a9wd_
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 (4 domains)

Domain ID domain_id2a9wA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
Domain ID domain_id2a9wB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
Domain ID domain_id2a9wC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
Domain ID domain_id2a9wD00
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)