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- PDB-1iq4: 5S-RRNA BINDING RIBOSOMAL PROTEIN L5 FROM BACILLUS STEAROTHERMOPHILUS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iq4 | ||||||
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Title | 5S-RRNA BINDING RIBOSOMAL PROTEIN L5 FROM BACILLUS STEAROTHERMOPHILUS | ||||||
![]() | 50S RIBOSOMAL PROTEIN L5 | ||||||
![]() | RNA BINDING PROTEIN / Ribosomal protein / rRNA-binding / RNP motif | ||||||
Function / homology | ![]() tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nakashima, T. / Yao, M. / Kawamura, S. / Iwasaki, K. / Kimura, M. / Tanaka, I. | ||||||
![]() | ![]() Title: Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding. Authors: Nakashima, T. / Yao, M. / Kawamura, S. / Iwasaki, K. / Kimura, M. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.1 KB | Display | ![]() |
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Full document | ![]() | 380.6 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 15.6 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20176.713 Da / Num. of mol.: 2 / Mutation: V9L, K10N, V111A, A121S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET22B / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.612 Å3/Da / Density % sol: 51.1 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG8000, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 252800 / Num. obs: 37507 / % possible obs: 97.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 36.99 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.046 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2239 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5384 / Rsym value: 0.203 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 252800 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.239 |
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Processing
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Refinement | Method to determine structure: ![]() ![]()
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Solvent computation | Bsol: 73.86 Å2 / ksol: 0.392 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.64 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 9.6 % / Rfactor obs: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 9.7 % |