+Open data
-Basic information
Entry | Database: PDB / ID: 1w40 | ||||||
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Title | T. celer L30e K9A variant | ||||||
Components | 50S RIBOSOMAL PROTEIN L30E | ||||||
Keywords | RIBOSOMAL PROTEIN / ELECTROSTATIC INTERACTIONS / THERMOSTABILITY / PROTEIN ENGINEERING | ||||||
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: 2.03 Å | ||||||
Authors | Lee, C.F. / Lee, K.M. / Chan, S.H. / Allen, M.D. / Bycroft, M. / Wong, K.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Electrostatic Interactions Contribute to Reduced Heat Capacity Change of Unfolding in a Thermophilic Ribosomal Protein L30E Authors: Lee, C.F. / Allen, M.D. / 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 | 1w40.cif.gz | 30.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w40.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w40_validation.pdf.gz | 417.5 KB | Display | wwPDB validaton report |
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Full document | 1w40_full_validation.pdf.gz | 418 KB | Display | |
Data in XML | 1w40_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1w40_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w40 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w40 | HTTPS FTP |
-Related structure data
Related structure data | 1w41C 1w42C 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: 10923.606 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS CELER (archaea) / Plasmid: PET8C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 PLYSS / References: UniProt: P29160 |
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#2: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.15 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→17 Å / Num. obs: 4994 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 13.9 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H7M Resolution: 2.03→32.11 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / SU B: 5.227 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.205 / 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: 11.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→32.11 Å
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Refine LS restraints |
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