4gev

E. coli thymidylate synthase Y209W variant in complex with substrate and a cofactor analog

Method: X-RAY DIFFRACTION Dmax: 73.5 Å Quality: EXCELLENT

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 Mutation:Y209W Non-standard monomer:Yes (specific site not provided by mmCIF) UMC 2'-deoxy-5'-uridylic acid × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;295 K;vapor diffusion against 1.44 M Sodium citrate, HEPES from 5.2 mg/ml protein solution containing 17mM kPO4, DTT, 3.3 mM dUMP, 3.3 mM CB3717 and either 0.5% ethylacetate or 4% N-propanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.30 Å R-free 0.151

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 Author chain B; 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 4gev

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gev
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gev
Deposition date deposition_date2012-08-02
Structure title titleE. coli thymidylate synthase Y209W variant in complex with substrate and a cofactor analog
Keywords keywordsbeta sheet, alpha/beta protein, methylase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.19
Radius of gyration Rg (electron density) rg_electron22.87
Forward intensity I(0) i064923300.00
Molecular weight molecular_weight62651.0 kDa
Excluded volume excluded_volume78096 ų
Envelope volume envelope_volume87713 ų
Hydration-shell volume shell_volume30662 ų
Envelope diameter envelope_diameter73.0
Shell Rg shell_rg31.14
Envelope Rg envelope_rg23.13
Shape Rg shape_rg22.87
Total Rg total_rg23.77
Total atoms total_atoms8664
Residues n_residues526
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 dmax73.5
Rg (real space) rg_real24.03
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real6.4920e+07
I(0) uncertainty (real space) i0_real_error7.6920e+05
Rg (reciprocal space) rg_reciprocal24.07
I(0) (reciprocal space) i0_reciprocal64920000.0000
Solution quality estimate total_estimate0.9043
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.0
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16070000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4geva_
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_idd4gevb_
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 (2 domains)

Domain ID domain_id4gevA00
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_id4gevB00
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 (2)

9. Files and Curves (10)