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- PDB-4qg3: Crystal structure of mutant ribosomal protein G219V TthL1 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qg3 | ||||||
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Title | Crystal structure of mutant ribosomal protein G219V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus | ||||||
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![]() | RIBOSOMAL PROTEIN/RNA / Rossmann Fold / RIBOSOMAL PROTEIN / rRNA / rRNA BINDING / RIBOSOME / RIBOSOMAL PROTEIN-RNA complex | ||||||
Function / homology | ![]() regulation of translation / cytosolic 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: Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions. Authors: Tishchenko, S. / Kostareva, O. / Gabdulkhakov, A. / Mikhaylina, A. / Nikonova, E. / Nevskaya, N. / Sarskikh, A. / Piendl, W. / 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 | ![]() | 113.3 KB | Display | ![]() |
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PDB format | ![]() | 80.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qgbC ![]() 4qviC ![]() 4reoC ![]() 3u4mS S: Starting model for refinement 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
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 24778.582 Da / Num. of mol.: 1 / Mutation: G219V 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 / Fragment: 80 nt fragment of 23S rRNA Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 279 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-IPA / #5: Chemical | ChemComp-BME / #6: Chemical | ChemComp-URE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.8 M Ammonium sulfate, 0.05 M Bis-Tris,pH 8.5, 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: Mar 1, 2013 |
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→50 Å / Num. all: 33273 / Num. obs: 33152 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3U4M Resolution: 2→22.981 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 22.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→22.981 Å
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Refine LS restraints |
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LS refinement shell |
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