+Open data
-Basic information
Entry | Database: PDB / ID: 1i4j | ||||||
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Title | CRYSTAL STRUCTURE OF L22 RIBOSOMAL PROTEIN MUTANT | ||||||
Components | 50S RIBOSOMAL PROTEIN L22 | ||||||
Keywords | RNA BINDING PROTEIN / Ribosomal Protein / Mutant / Erythromycin Resistance / RNA binding | ||||||
Function / homology | Function and homology information large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Davydova, N.L. / Streltsov, V.A. / Fedorov, R. / Wilce, M. / Liljas, A. / Garder, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: L22 ribosomal protein and effect of its mutation on ribosome resistance to erythromycin. Authors: Davydova, N. / Streltsov, V. / Wilce, M. / Liljas, A. / Garber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i4j.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i4j.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i4j ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i4j | HTTPS FTP |
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-Related structure data
Related structure data | 1bxeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12348.404 Da / Num. of mol.: 2 / Mutation: DEL(82-84) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: RPL22 / Plasmid: PTTHL22 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48286 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.9M Sodium chloride, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 5.5 Details: Davydova, N., (2001) Acta Crystallogr., Sect.D, 57, 1150. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: monochromator and mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23.17 Å / Num. all: 16162 / Num. obs: 16162 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 34.7 Å2 / Limit h max: 17 / Limit h min: -17 / Limit k max: 46 / Limit k min: -17 / Limit l max: 20 / Limit l min: 0 / Observed criterion F max: 475552.48 / Observed criterion F min: 0.45 / Rmerge(I) obs: 0.074 / Net I/σ(I): 74.7 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 71.3 / Num. unique all: 1235 / % possible all: 47.3 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 23.2 Å / Redundancy: 4 % / Num. measured all: 64827 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 47.3 % / Redundancy: 3 % / Num. unique obs: 1334 / Rmerge(I) obs: 0.331 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BXE WITH REMOVED BETA-LOOP Resolution: 1.8→23.17 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.43 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 59.4316 Å2 / ksol: 0.369737 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.24 Å2 / Biso mean: 37.8 Å2 / Biso min: 12.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→23.17 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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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor all: 0.208 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.283 |