[English] 日本語
Yorodumi- PDB-7mln: Crystal structure of ricin A chain in complex with 5-(o-tolyl)thi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mln | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ricin A chain in complex with 5-(o-tolyl)thiophene-2-carboxylic acid | ||||||
Components | Ricin | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Ricin chain-A / RTA / Hydrolase / Toxin / Inhibitor / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | Ricinus communis (castor bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Harijan, R.K. / Li, X.P. / Cao, B. / Augeri, D. / Bonanno, J.B. / Almo, S.C. / Tumer, N.E. / Schramm, V.L. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. Authors: Li, X.P. / Harijan, R.K. / Cao, B. / Kahn, J.N. / Pierce, M. / Tsymbal, A.M. / Roberge, J.Y. / Augeri, D. / Tumer, N.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mln.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mln.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 7mln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mln_validation.pdf.gz | 726.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7mln_full_validation.pdf.gz | 727.6 KB | Display | |
Data in XML | 7mln_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 7mln_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7mln ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7mln | HTTPS FTP |
-Related structure data
Related structure data | 7mloC 7mlpC 7mltC 1rtcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 30067.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ZJA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 24 %(w/v) PEG 1500, 20 %(w/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→62.21 Å / Num. obs: 43433 / % possible obs: 99.8 % / Redundancy: 7 % / CC1/2: 0.99 / Rpim(I) all: 0.02 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.52→1.55 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2095 / CC1/2: 0.65 / Rpim(I) all: 0.41 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTC Resolution: 1.52→62.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.755 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.41 Å2 / Biso mean: 30.461 Å2 / Biso min: 16.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→62.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|