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Yorodumi- PDB-5zei: Crystal structure of the bacterial A1408me1A-mutant ribosomal dec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zei | ||||||||||||||||||||||||
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Title | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin | ||||||||||||||||||||||||
Components |
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Keywords | RNA / ribosome / aminoglycoside / antibiotic-resistance | ||||||||||||||||||||||||
Function / homology | GENETICIN / RNA / RNA (> 10) Function and homology information | ||||||||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||||||||||||||
Authors | Kanazawa, H. / Baba, F. / Koganei, M. / Kondo, J. | ||||||||||||||||||||||||
Funding support | Japan, 7items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA. Authors: Kanazawa, H. / Baba, F. / Koganei, M. / Kondo, J. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zei.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zei.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zei_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5zei_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5zei_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 5zei_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5zei ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5zei | HTTPS FTP |
-Related structure data
Related structure data | 5zegC 5zejC 5zemC 3td1S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 7063.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: RNA chain | Mass: 6757.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium cacodylate, Spermine, MPD, ammonium chloride |
-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 315r / Detector: CCD / Date: May 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.9 Å / Num. obs: 8419 / % possible obs: 96.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.365 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TD1 Resolution: 2.1→44.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.69 Å2 / Biso mean: 39.21 Å2 / Biso min: 23.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→44.9 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: 6
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