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Yorodumi- PDB-2vpl: The structure of the complex between the first domain of L1 prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vpl | ||||||
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Title | The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii | ||||||
Components |
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Keywords | TRANSLATION / RIBOSOMAL PROTEIN / RNA-PROTEIN COMPLEX / TRANSLATION REGULATION / REPRESSOR / RNA-BINDING / TRNA-BINDING / RRNA-BINDING | ||||||
Function / homology | Function and homology information regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) METHANOCALDOCOCCUS JANNASCHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kljashtorny, V. / Tishchenko, S. / Nevskaya, N. / Nikonov, S. / Garber, M. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2008 Title: Domain II of Thermus thermophilus ribosomal protein L1 hinders recognition of its mRNA. Authors: Tishchenko, S. / Kljashtorny, V. / Kostareva, O. / Nevskaya, N. / Nikulin, A. / Gulak, P. / Piendl, W. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vpl.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vpl.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vpl_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 2vpl_full_validation.pdf.gz | 479.9 KB | Display | |
Data in XML | 2vpl_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2vpl_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vpl ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vpl | HTTPS FTP |
-Related structure data
Related structure data | 2hw8S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15171.353 Da / Num. of mol.: 2 / Fragment: FIRST DOMAIN, RESIDUES 2-68,160-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P27150 #2: RNA chain | Mass: 15522.342 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea) Production host: ESCHERICHIA COLI (E. coli) #3: Chemical | #4: 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: 2.44 Å3/Da / Density % sol: 49 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 |
Detector | Type: MARRRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 26880 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.6 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HW8 Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.265 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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