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- PDB-3u4m: Crystal structure of ribosomal protein tthl1 in complex with 80nt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u4m | ||||||
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Title | Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus | ||||||
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![]() | RNA/RNA BINDING PROTEIN / Rossmann Fold / RIBOSOMAL PROTEIN / rRNA / rRNA BINDING / RIBOSOME / RNA-RNA BINDING PROTEIN complex | ||||||
Function / homology | ![]() regulation of translation / large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Nevskaya, N.A. / NIkonov, S.V. | ||||||
![]() | ![]() Title: High-resolution crystal structure of the isolated ribosomal L1 stalk. Authors: Tishchenko, S. / Gabdulkhakov, A. / Nevskaya, N. / Sarskikh, A. / Kostareva, O. / Nikonova, E. / Sycheva, A. / Moshkovskii, S. / Garber, M. / 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 | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 81.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.1 KB | Display | ![]() |
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Full document | ![]() | 490.2 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 24867.699 Da / Num. of mol.: 1 / Mutation: V218R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 25974.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: fragment of 23S rRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 6 types, 224 molecules 










#3: Chemical | #4: Chemical | ChemComp-MLI / #5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 50mM NaCl, 2.5M Ammonium sulfate, 50mM MES, 10mM Magnesium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 18, 2010 |
Radiation | Monochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20.67 Å / Num. all: 35285 / Num. obs: 33346 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.99 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.064 / Net I/σ(I): 19.14 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 6.68 / Num. unique all: 4415 / Rsym value: 0.169 / % possible all: 89.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 1AD2, 1MZP Resolution: 2→19.675 Å / SU ML: 0.23 / σ(F): 2.08 / Phase error: 18.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.589 Å2 / ksol: 0.454 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→19.675 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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