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Yorodumi- PDB-1i6u: RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i6u | ||||||
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Title | RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII | ||||||
Components |
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Keywords | RIBOSOME / protein-RNA interactions / ribosomal protein S8 / RNA | ||||||
Function / homology | Function and homology information cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Tishchenko, S. / Nikulin, A. / Fomenkova, N. / Nevskaya, N. / Nikonov, O. / Dumas, P. / Moine, H. / Ehresmann, B. / Ehresmann, C. / Piendl, W. ...Tishchenko, S. / Nikulin, A. / Fomenkova, N. / Nevskaya, N. / Nikonov, O. / Dumas, P. / Moine, H. / Ehresmann, B. / Ehresmann, C. / Piendl, W. / Lamzin, V. / Garber, M. / Nikonov, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii. Authors: Tishchenko, S. / Nikulin, A. / Fomenkova, N. / Nevskaya, N. / Nikonov, O. / Dumas, P. / Moine, H. / Ehresmann, B. / Ehresmann, C. / Piendl, W. / Lamzin, V. / Garber, M. / Nikonov, S. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site. Authors: Nevskaya, N. / Tishchenko, S. / Nikulin, A. / al-Karadaghi, S. / Liljas, A. / Ehresmann, B. / Ehresmann, C. / Garber, M. / Nikonov, S. #2: Journal: J.Mol.Biol. / Year: 1998 Title: NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA Authors: Kalurachci, K. / Nikonowicz, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6u.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6u.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 1i6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6u ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6u | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 11894.089 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The rRNA fragment was obtained by transcription from synthetic DNA template using T7 RNA polymerase. #2: Protein | Mass: 14744.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJAS8 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P54041 #3: Chemical | ChemComp-SO4 / #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: 4.79 Å3/Da / Density % sol: 74.34 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulphate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.57→41.07 Å / Num. all: 30271 / Num. obs: 30271 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13 | ||||||||||||||||||||||||
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.249 / % possible all: 82.5 | ||||||||||||||||||||||||
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→41.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1361993.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.43 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→41.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 4.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.379 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.343 |