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- PDB-1mji: DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mji | ||||||
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Title | DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX | ||||||
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![]() | RIBOSOME / ribosomal protein - 5S rRNA complex | ||||||
Function / homology | ![]() cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perederina, A. / Nevskaya, N. / Nikonov, O. / Nikulin, A. / Dumas, P. / Yao, M. / Tanaka, I. / Garber, M. / Gongadze, G. / Nikonov, S. | ||||||
![]() | ![]() Title: Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex Authors: Perederina, A. / Nevskaya, N. / Nikonov, O. / Nikulin, A. / Dumas, P. / Yao, M. / Tanaka, I. / Garber, M. / Gongadze, G. / Nikonov, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.1 KB | Display | ![]() |
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PDB format | ![]() | 97.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
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Full document | ![]() | 497.1 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: RNA chain | Mass: 10847.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 21155.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate, magnesium acetate, potassium chlorate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 22650 / Num. obs: 22650 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1908 / % possible all: 84.1 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 22852 / % possible obs: 99.9 % / Redundancy: 3.02 % |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 84.1 % / Redundancy: 3 % / Num. unique obs: 1908 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.9597 Å2 / ksol: 0.324816 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.44 Å / Luzzati sigma a free: 0.44 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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