7mlo

Crystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic acid

Method: X-RAY DIFFRACTION Dmax: 91.0 Å Quality: GOOD

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

Ricin

Ricinus communis

UniProt P02879

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 36–302 Not recorded ZJ7 5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;50 mM Bis-Tris pH 6.5, 50 mM Ammonium Sulfate, 30 %(v/v) Pentaerythritol Ethoxylate (15/4 EO/OH) Resolution 1.65 Å R-free 0.237
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 36–302 Not recorded ZJ7 5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;50 mM Bis-Tris pH 6.5, 50 mM Ammonium Sulfate, 30 %(v/v) Pentaerythritol Ethoxylate (15/4 EO/OH) Resolution 1.65 Å R-free 0.237

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.

100 other PDB entries and 125 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RICI_RICCO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–268; UniProt 36–302 Author chain B; PDBConstruct 2–268; UniProt 36–302

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 7mlo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7mlo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7mlo
Deposition date deposition_date2021-04-28
Structure title titleCrystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic acid
Keywords keywordsRicin chain-A, RTA, Hydrolase, Toxin, Inhibitor, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.41
Radius of gyration Rg (electron density) rg_electron26.61
Forward intensity I(0) i055237100.00
Molecular weight molecular_weight58300.0 kDa
Excluded volume excluded_volume73007 ų
Envelope volume envelope_volume87104 ų
Hydration-shell volume shell_volume28113 ų
Envelope diameter envelope_diameter93.1
Shell Rg shell_rg33.31
Envelope Rg envelope_rg26.73
Shape Rg shape_rg26.65
Total Rg total_rg27.18
Total atoms total_atoms4116
Residues n_residues518
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 dmax91.0
Rg (real space) rg_real27.56
Rg uncertainty (real space) rg_real_error0.91
I(0) (real space) i0_real5.5240e+07
I(0) uncertainty (real space) i0_real_error9.5630e+05
Rg (reciprocal space) rg_reciprocal27.52
I(0) (reciprocal space) i0_reciprocal55240000.0000
Solution quality estimate total_estimate0.8675
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3
Skewness Skewness skewness0.497
Kurtosis Kurtosis kurtosis-0.293
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12710000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.797; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.930

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)