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Yorodumi- PDB-5z71: Crystal structure of the Homo Sapiens cytoplasmic ribosomal decod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z71 | ||||||||||||||||||||
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Title | Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form) | ||||||||||||||||||||
Components | RNA (5'-R(P*Keywords | RNA / ribosome / decoding site / G418 | Function / homology | GENETICIN / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | Authors | Kanazawa, H. / Tsurumi, N. / Kondo, J. | Citation | Journal: To Be Published | Title: Structural studies of aminoglycoside antibiotics G418 and its derivatives with readthrough activities Authors: Kanazawa, H. / Tsurumi, N. / Baasov, T. / Kondo, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z71.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z71.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 5z71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z71_validation.pdf.gz | 733.1 KB | Display | wwPDB validaton report |
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Full document | 5z71_full_validation.pdf.gz | 734 KB | Display | |
Data in XML | 5z71_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 5z71_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/5z71 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/5z71 | HTTPS FTP |
-Related 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: 7049.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-GET / | #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: 2.31 Å3/Da / Density % sol: 46.7 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: MPD, Sodium chloride, Sprimine 4HCl, Sodium cacodylate (pH 5.0) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 10, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→45.053 Å / Num. obs: 8669 / % possible obs: 98.9 % / Redundancy: 3.827 % / Biso Wilson estimate: 65.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.034 / Χ2: 1.087 / Net I/σ(I): 25.53 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.5→45.053 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.31 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.79 Å2 / Biso mean: 63.5 Å2 / Biso min: 41.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→45.053 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: 7
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