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- PDB-3bnp: 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: 3bnp | ||||||
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Title | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G Mutant) | ||||||
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![]() | RNA / ribosome / decoding site | ||||||
Function / homology | : / 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 | ![]() | 31.9 KB | Display | ![]() |
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PDB format | ![]() | 22.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.5 KB | Display | ![]() |
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Full document | ![]() | 403.3 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bnlC ![]() 3bnnC ![]() 3bnoC ![]() 3bnqC ![]() 3bnrC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 7023.250 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically |
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#2: RNA chain | Mass: 6718.068 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium cacodylate, KCl, glycerol, 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: Mar 17, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→40.59 Å / Num. obs: 4215 / % possible obs: 99.5 % / Redundancy: 9.94 % / Rmerge(I) obs: 0.065 / Χ2: 0.99 / Net I/σ(I): 22 / Scaling rejects: 317 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 68.858 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 77.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40.59 Å
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Refine LS restraints |
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Xplor file |
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