+Open data
-Basic information
Entry | Database: PDB / ID: 1w3e | ||||||
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Title | Ribosomal L30e of Thermococcus celer, P59A mutant | ||||||
Components | 50S RIBOSOMAL PROTEIN L30E | ||||||
Keywords | RIBOSOMAL PROTEIN / THERMAL STABLE | ||||||
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: 1.77 Å | ||||||
Authors | Ma, H.W. / Lee, C.F. / Allen, M.D. / Bycroft, M. / Wong, K.B. | ||||||
Citation | Journal: To be Published Title: Role of Proline Residues in Thermostability of T. Celer L30E Protein Authors: Ma, H.W. / Lee, C.F. / Allen, M.D. / Bycroft, M. / Wong, K.B. #1: Journal: Protein Sci. / Year: 2003 Title: Solution Structure and Thermal Stability of Ribosomal Protein L30E from Hyperthermophilic Archaeon Thermococcus Celer Authors: Wong, K.B. / Lee, C.F. / Chan, S.H. / Leung, T.Y. / Chen and M Bycroft, Y.W. #2: Journal: Biochemistry / Year: 2003 Title: Crystal Structure of Ribosomal Protein L30E from the Extreme Thermophile Thermococcus Celer: Thermal Stability and RNA Binding. Authors: Chen, Y.W. / Bycroft, M. / 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 | 1w3e.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w3e.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 1w3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w3e ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w3e | HTTPS FTP |
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-Related structure data
Related structure data | 1h7mS 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: 10955.672 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS CELER (archaea) / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P29160 |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 36 % |
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Crystal grow | pH: 7 / Details: 10% PEG 6000 0.1M HEPES PH 7.0 20% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→16.93 Å / Num. obs: 7622 / % possible obs: 99.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.77→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 11.7 / % possible all: 98.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H7M Resolution: 1.77→32.27 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.827 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME ATOMS OF ARG 92 NOT MODELLED BECAUSE NO ELECTRON DENSITY APPARENT AROUND THE RESIDUE
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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: 12.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→32.27 Å
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Refine LS restraints |
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