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Yorodumi- PDB-1lc4: Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lc4 | ||||||||||||||||||
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Title | Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / Antibiotic-RNA complex / adenine bulges | Function / homology | TOBRAMYCIN / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | Authors | Vicens, Q. / Westhof, E. | Citation | Journal: Chem.Biol. / Year: 2002 Title: Crystal Structure of a Complex between the Aminoglycoside Tobramycin and an Oligonucleotide Containing the Ribosomal Decoding A Site Authors: Vicens, Q. / Westhof, E. #1: Journal: Structure / Year: 2001 Title: Crystal Structure of Paromomycin Docked into the Eubacterial Ribosomal Decoding A Site Authors: Vicens, Q. / Westhof, E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lc4.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lc4.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lc4_validation.pdf.gz | 718.9 KB | Display | wwPDB validaton report |
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Full document | 1lc4_full_validation.pdf.gz | 719.9 KB | Display | |
Data in XML | 1lc4_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 1lc4_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lc4 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lc4 | HTTPS FTP |
-Related structure data
Related structure data | 1j7tS 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
#1: RNA chain | Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: eubacterial 16S RRNA A SITE #2: Chemical | #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: 2.59 Å3/Da / Density % sol: 52.46 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MPD, sodium cacodylate, sodium chloride, potassium chloride, magnesium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2001 Details: double crystal monochromator and toroidal focusing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→10 Å / Num. all: 4899 / % possible obs: 95.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 62.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.54→2.64 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 9.2 / Num. unique all: 479 / Rsym value: 0.133 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 4899 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.133 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J7T Resolution: 2.54→10 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1338987.24 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 1.5 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.7193 Å2 / ksol: 0.284702 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.54→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.7 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 7.5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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