+Open data
-Basic information
Entry | Database: PDB / ID: 1dwu | ||||||
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Title | Ribosomal protein L1 | ||||||
Components | RIBOSOMAL PROTEIN L1 | ||||||
Keywords | RIBOSOMAL PROTEIN / RNA BINDING / PROTEIN SYNTHESIS | ||||||
Function / homology | Function and homology information large ribosomal subunit / regulation of translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | METHANOCOCCUS THERMOLITHOTROPHICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tishchenko, S.V. / Nevskaya, N.A. / Pavelyev, M.N. / Nikonov, S.V. / Garber, M.B. / Piendl, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of Ribosomal Protein L1 from Methanococcus Thermolithotrophicus. Functionally Important Structural Invariants on the L1 Surface Authors: Nevskaya, N.A. / Tishchenko, S.V. / Paveliev, M. / Smolinskaya, Y. / Fedorov, R. / Piendl, W. / Nakamura, Y. / Toyoda, T. / Garber, M.B. / Nikonov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dwu.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dwu.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dwu_validation.pdf.gz | 417.2 KB | Display | wwPDB validaton report |
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Full document | 1dwu_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 1dwu_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1dwu_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/1dwu ftp://data.pdbj.org/pub/pdb/validation_reports/dw/1dwu | HTTPS FTP |
-Related structure data
Related structure data | 1cjsS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23831.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOCOCCUS THERMOLITHOTROPHICUS (archaea) Strain: SN-1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Cellular location: RIBOSOME / Gene: THE CORRESPONDING GENE IN E. COLI IS RPLA / Plasmid: PMTHL1.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52704 |
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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: 2.63 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 10% PEG 4K, 40MM MGCL2, 50MM NAAC PH 5.5, 50MM NACL, AGAINST: 30% PEG 4K, 100 MM NAAC | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: R-AXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→31.01 Å / Num. obs: 13590 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.31 % / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.68→2.77 Å / % possible all: 78.3 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. obs: 14280 / % possible obs: 94.6 % / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 81.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.275 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CJS Resolution: 2.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: X-PLOR V3.1F WAS ALSO USED.
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Displacement parameters | Biso mean: 37.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. reflection obs: 12624 / % reflection Rfree: 8.9 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 53 Å2 |