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- PDB-3bnr: Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Dec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bnr | ||||||
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Title | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative) | ||||||
![]() | (A site of human mitochondrial ribosome, chain ...) x 3 | ||||||
![]() | RNA / ribosome / decoding site | ||||||
Function / homology | : / PAROMOMYCIN / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kondo, J. / Westhof, E. | ||||||
![]() | ![]() Title: The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates Authors: Kondo, J. / Westhof, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.1 KB | Display | ![]() |
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Full document | ![]() | 807.9 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bnlC ![]() 3bnnC ![]() 3bnoC ![]() 3bnpC ![]() 3bnqC ![]() 3bnsC ![]() 3bntC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-A site of human mitochondrial ribosome, chain ... , 3 types, 4 molecules ACBD
#1: RNA chain | Mass: 7394.280 Da / Num. of mol.: 2 / Mutation: A1555G / Source method: obtained synthetically #2: RNA chain | | Mass: 7088.115 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically #3: RNA chain | | Mass: 6781.949 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically |
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-Non-polymers , 3 types, 186 molecules ![](data/chem/img/K.gif)
![](data/chem/img/PAR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PAR.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-PAR / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.81 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium cacodylate, KCl, spermine tetrachloride, paromomycin, 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 20, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50.995 Å / Num. obs: 16388 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 2.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 69.092 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 36.922 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50.995 Å
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Refine LS restraints |
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Xplor file |
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