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Yorodumi- PDB-1j7t: Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j7t | ||||||||||||||||||
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Title | Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / RNA-aminoglycoside interactions / A site / UoU pairs / AA bulges | Function / homology | PAROMOMYCIN / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | Authors | Vicens, Q. / Westhof, E. | Citation | 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 | 1j7t.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7t.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1j7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7t ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7t | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7048.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Escherichia coli 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: 2.56 Å3/Da / Density % sol: 51.95 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MPD, NaCl, MgSO4, glycerol, Na cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 28, 2000 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 5144 / Num. obs: 5144 / % possible obs: 95 % / Redundancy: 9.7 % / Rsym value: 0.055 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.23 / % possible all: 97.4 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 5278 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model containing the 16S rRNA A site as solved in the crystallographic structure of the 30S ribosomal particle complexed to paromomycin Resolution: 2.5→15 Å / Isotropic thermal model: isotropic / 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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Displacement parameters | Biso mean: 52.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 7.5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.206 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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