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Yorodumi- PDB-5zem: Crystal structure of the bacterial A1408me1A-mutant ribosomal dec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zem | |||||||||||||||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicin | |||||||||||||||||||||||||||||||||||||||||||||||||
Components | RNA (5'-R(P*Keywords | RNA / ribosome / aminoglycoside / antibiotic-resistance | Function / homology | RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.103 Å | Authors | Kanazawa, H. / Baba, F. / Koganei, M. / Kondo, J. | Funding support | Japan, 7items |
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 | 5zem.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zem.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zem_validation.pdf.gz | 411.2 KB | Display | wwPDB validaton report |
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Full document | 5zem_full_validation.pdf.gz | 412.6 KB | Display | |
Data in XML | 5zem_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 5zem_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5zem ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5zem | HTTPS FTP |
-Related structure data
Related structure data | 5zegC 5zeiC 5zejC 3td1S 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 7063.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: 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: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium cacodylate, spermine, MPD, Potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→42.3 Å / Num. obs: 2851 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13 |
Reflection shell | Resolution: 3.1→3.2 Å / Rmerge(I) obs: 0.284 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TD1 Resolution: 3.103→42.3 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 35.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 258.83 Å2 / Biso mean: 107.83 Å2 / Biso min: 75.21 Å2 | |||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.103→42.3 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: 2
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