9dt3

Crystal structure of the engineered sulfonylurea repressor EsR (L11-C6), bound to ethametsulfuron-methyl

Method: X-RAY DIFFRACTION Dmax: 108.2 Å Quality: GOOD

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

Sulfonylurea repressor EsR (L11-C6)

Escherichia coli

UniProt P04483

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 1–207 Chain B; UniProt 1–207 Not recorded RXF methyl 2-[[4-ethoxy-6-(methylamino)-1,3,5-triazin-2-yl]carbamoylsulfamoyl]benzoate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.05 M Magnesium chloride 0.1 M HEPES pH 7.5 30% v/v Polyethylene glycol monomethyl ether 550 Resolution 2.80 Å R-free 0.278
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–207 Chain D; UniProt 1–207 Not recorded RXF methyl 2-[[4-ethoxy-6-(methylamino)-1,3,5-triazin-2-yl]carbamoylsulfamoyl]benzoate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.05 M Magnesium chloride 0.1 M HEPES pH 7.5 30% v/v Polyethylene glycol monomethyl ether 550 Resolution 2.80 Å R-free 0.278

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.

17 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TETR2_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–207; UniProt 1–207 Author chain B; PDBConstruct 1–207; UniProt 1–207 Author chain C; PDBConstruct 1–207; UniProt 1–207 Author chain D; PDBConstruct 1–207; UniProt 1–207

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 9dt3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dt3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dt3
Deposition date deposition_date2024-09-30
最后修订 last_revision2025-10-08
Structure title titleCrystal structure of the engineered sulfonylurea repressor EsR (L11-C6), bound to ethametsulfuron-methyl
Keywords keywordsrepressor, transcription, TetR, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.75
Radius of gyration Rg (electron density) rg_electron32.38
Forward intensity I(0) i0123085000.00
Molecular weight molecular_weight87660.0 kDa
Excluded volume excluded_volume109600 ų
Envelope volume envelope_volume145600 ų
Hydration-shell volume shell_volume38626 ų
Envelope diameter envelope_diameter114.9
Shell Rg shell_rg38.28
Envelope Rg envelope_rg31.84
Shape Rg shape_rg32.45
Total Rg total_rg32.65
Total atoms total_atoms6156
Residues n_residues770
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 dmax108.2
Rg (real space) rg_real32.87
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real1.2310e+08
I(0) uncertainty (real space) i0_real_error2.1140e+06
Rg (reciprocal space) rg_reciprocal32.82
I(0) (reciprocal space) i0_reciprocal123100000.0000
Solution quality estimate total_estimate0.8783
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.8
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29280000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.850

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)