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Yorodumi- PDB-2bee: Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bee | ||||||||||||||||||||
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Title | Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA/antibiotic / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES / RNA-antibiotic complex | Function / homology | Chem-JS4 / RNA / RNA (> 10) | Function and homology information Biological species | Streptomyces rimosus subsp. paromomycinus (bacteria) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | Authors | Francois, B. / Westhof, E. | Citation | Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2004 | Title: Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site Authors: Francois, B. / Szychowski, J. / Adhikari, S.S. / Pachamuthu, K. / Swayze, E.E. / Griffey, R.H. / Migawa, M.T. / Westhof, E. / Hanessian, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bee.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bee.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 2bee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bee_validation.pdf.gz | 995.4 KB | Display | wwPDB validaton report |
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Full document | 2bee_full_validation.pdf.gz | 1004.5 KB | Display | |
Data in XML | 2bee_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 2bee_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2bee ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bee | HTTPS FTP |
-Related structure data
Related structure data | 2be0C 1j7tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7048.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Eubacterial 16S Rrna A Site Source: (synth.) Streptomyces rimosus subsp. paromomycinus (bacteria) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MPD, KCl, MGSO4, GLYCEROL, Na Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→50 Å / Num. all: 34644 / Num. obs: 34100 / % possible obs: 98 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7 % |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J7T Resolution: 2.6→30 Å / σ(F): 2 Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY,A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERSFOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52,57-64 (1996)
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / % reflection obs: 100 % |