[English] 日本語
Yorodumi- PDB-3s4p: Crystal structure of the bacterial ribosomal decoding site comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s4p | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogue | ||||||||||||||||||
Components | RNA (5'-R(P*Keywords | RNA/ANTIBIOTIC / aminoglycoside / antibiotics / ribosome / decoding site / RNA / RNA-ANTIBIOTIC complex | Function / homology | Chem-JS6 / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 Å | Authors | Szychowski, J. / Kondo, J. / Zahr, O. / Auclair, K. / Westhof, E. / Hanessian, S. / Keillor, J.W. | Citation | Journal: Chemmedchem / Year: 2011 | Title: Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues Authors: Szychowski, J. / Kondo, J. / Zahr, O. / Auclair, K. / Westhof, E. / Hanessian, S. / Keillor, J.W. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3s4p.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3s4p.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s4p_validation.pdf.gz | 950.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3s4p_full_validation.pdf.gz | 961.1 KB | Display | |
Data in XML | 3s4p_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 3s4p_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/3s4p ftp://data.pdbj.org/pub/pdb/validation_reports/s4/3s4p | HTTPS FTP |
-Related structure data
Related structure data | 1j7tS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 6743.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium Cacodylate, Spermine, KCl, MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→40.4 Å / Num. obs: 5003 / % possible obs: 99.6 % |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J7T Resolution: 2.56→10 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8273 / σ(F): 65
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 36.3817 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.19 Å2 / Biso mean: 47.9676 Å2 / Biso min: 14.54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|