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Yorodumi- PDB-6jbf: Crystal structure of the bacterial ribosomal decoding site in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jbf | ||||||||||||||||||||||||||||||||||
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Title | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) | ||||||||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA/ANTIBIOTIC / RNA / antibiotic / RNA-ANTIBIOTIC complex | Function / homology | Chem-V71 / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | Authors | Kanazawa, H. / Auffinger, P. / Hanessian, S. / Kondo, J. | Funding support | Japan, 1items |
Citation | Journal: To Be Published | Title: Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) Authors: Kondo, J. / Hanessian, S. / Kanazawa, H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jbf.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jbf.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/6jbf ftp://data.pdbj.org/pub/pdb/validation_reports/jb/6jbf | HTTPS FTP |
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-Related structure data
Related structure data | 6jbgC 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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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7370.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Sugar | ChemComp-V71 / ( | #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 % sol: 34.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 3350, NaCl, spermine tetrahydrochloride, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 9, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→42.543 Å / Num. obs: 6744 / % possible obs: 99.8 % / Redundancy: 6.782 % / Biso Wilson estimate: 35.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 0.993 / Net I/σ(I): 25.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J7T Resolution: 2.6→42.543 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.41 Å2 / Biso mean: 32.58 Å2 / Biso min: 13.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→42.543 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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