+Open data
-Basic information
Entry | Database: PDB / ID: 3lfo | ||||||
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Title | Crystal structure of T. celer L30e E90A/R92A variant | ||||||
Components | 50S ribosomal protein L30e | ||||||
Keywords | RIBOSOMAL PROTEIN / L30e / Thermophilic / globular protein | ||||||
Function / homology | Function and homology information cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding Similarity search - Function | ||||||
Biological species | Thermococcus celer (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chan, C.H. / Wong, K.B. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. Authors: Chan, C.H. / Yu, T.H. / Wong, K.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lfo.cif.gz | 32.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lfo.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 3lfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lfo_validation.pdf.gz | 416.6 KB | Display | wwPDB validaton report |
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Full document | 3lfo_full_validation.pdf.gz | 416.5 KB | Display | |
Data in XML | 3lfo_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 3lfo_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/3lfo ftp://data.pdbj.org/pub/pdb/validation_reports/lf/3lfo | HTTPS FTP |
-Related structure data
Related structure data | 3ra5C 3ra6C 1h7mS S: Starting model for refinement C: citing same article (ref.) |
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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: 10837.557 Da / Num. of mol.: 1 / Mutation: E90A, R92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus celer (archaea) / Gene: rpl30e, rpl30 / Plasmid: pET3C / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P29160 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 18% PEG 3350, 0.1M sodium citrate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2007 / Details: VariMax HR optics |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.72 Å / Num. obs: 7279 / % possible obs: 98.1 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1034 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H7M Resolution: 1.8→31.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.811 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.144 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.713 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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