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Yorodumi- PDB-7edl: Crystal structure of the bacterial ribosomal decoding site in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7edl | ||||||||||||||||||||||||||||
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Title | Crystal structure of the bacterial ribosomal decoding site in complex with G418 and Hg(II) | ||||||||||||||||||||||||||||
Components | RNA (5'-R(P*Keywords | RNA / Metal-mediated base pair / Mercury / Decoding site / Ribosomal RNA | Function / homology | GENETICIN / : / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | Authors | Kondo, J. / Suzuki, C. | Funding support | Japan, 1items |
Citation | Journal: To Be Published | Title: Crystal structure of the prokaryotic ribosomal decoding site in complex with G418 and Hg(II) Authors: Kondo, J. / Suzuki, C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7edl.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7edl.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 7edl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7edl_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7edl_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7edl_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 7edl_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/7edl ftp://data.pdbj.org/pub/pdb/validation_reports/ed/7edl | HTTPS FTP |
-Related structure data
Related structure data | 4k32S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7370.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium cacodylate, MPD, sodium chloride, spermine tetrahydrochloride, G418, mercury(II) perchlorate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 23, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→48.65 Å / Num. obs: 8525 / % possible obs: 99.3 % / Redundancy: 3.516 % / Biso Wilson estimate: 50.008 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.065 / Χ2: 1.04 / Net I/σ(I): 15.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4k32 Resolution: 2.6→48.65 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.68 / Stereochemistry target values: ML Details: The SF file contains friedel pairs under F_plus and F_minus columns.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.74 Å2 / Biso mean: 40.6951 Å2 / Biso min: 22.24 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %
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