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Yorodumi- PDB-4k32: Crystal structure of geneticin bound to the leishmanial rRNA A-site -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k32 | ||||||||||||||||||||
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Title | Crystal structure of geneticin bound to the leishmanial rRNA A-site | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA/antibiotic / rRNA duplex / Ribosomal A-site / Aminoglycoside / Leishmanial ribosome / RNA / RNA-antibiotic complex | Function / homology | GENETICIN / RNA / RNA (> 10) | Function and homology information Biological species | Leishmania (eukaryote) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | Authors | Shalev, M. / Kondo, J. / Adir, N. / Baasov, T. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 | Title: Identification of the molecular attributes required for aminoglycoside activity against Leishmania. Authors: Shalev, M. / Kondo, J. / Kopelyanskiy, D. / Jaffe, C.L. / Adir, N. / Baasov, T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k32.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k32.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k32_validation.pdf.gz | 1017.5 KB | Display | wwPDB validaton report |
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Full document | 4k32_full_validation.pdf.gz | 1020 KB | Display | |
Data in XML | 4k32_validation.xml.gz | 4 KB | Display | |
Data in CIF | 4k32_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/4k32 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/4k32 | HTTPS FTP |
-Related 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: 7356.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Leishmania (eukaryote) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1-20% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-200 mM KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9394 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 21134 / Num. obs: 4294 / % possible obs: 81.6 % / Observed criterion σ(F): 21.5 / Observed criterion σ(I): 21.5 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 2.5→2.57 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→23.505 Å / SU ML: 0.41 / σ(F): 2.04 / Phase error: 25.06 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.954 Å2 / ksol: 0.403 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→23.505 Å
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Refine LS restraints |
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LS refinement shell |
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