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Yorodumi- PDB-1y69: RRF domain I in complex with the 50S ribosomal subunit from Deino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y69 | ||||||
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Title | RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans | ||||||
Components |
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Keywords | RIBOSOME / 50S / RRF / RECYCLING FACTOR | ||||||
Function / homology | Function and homology information cytoplasmic translational termination / ribosomal large subunit binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Deinococcus radiodurans R1 (radioresistant) Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.33 Å | ||||||
Authors | Wilson, D.N. / Schluenzen, F. / Harms, J.M. / Yoshida, T. / Ohkubo, T. / Albrecht, R. / Buerger, J. / Kobayashi, Y. / Fucini, P. | ||||||
Citation | Journal: EMBO J. / Year: 2005 Title: X-ray crystallography on ribosome recycling: mechanism of binding and action of RRF on the 50S ribosomal subunit Authors: Wilson, D.N. / Schluenzen, F. / Harms, J.M. / Yoshida, T. / Ohkubo, T. / Albrecht, R. / Buerger, J. / Kobayashi, Y. / Fucini, P. | ||||||
History |
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Remark 999 | SEQUENCE Domain II of RRF (residues 31-105) was replaced by GLY-GLY-GLY |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y69.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1y69.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1y69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y69 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y69 | HTTPS FTP |
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-Related structure data
Related structure data | 1nkwS 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: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans R1 (radioresistant) References: GenBank: 1026245073 |
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#2: RNA chain | Mass: 39911.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans R1 (radioresistant) References: GenBank: 11612676 |
#3: Protein | Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 References: UniProt: Q9RXJ5 |
#4: Protein | Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 References: UniProt: Q9RY65 |
#5: Protein | Mass: 12844.616 Da / Num. of mol.: 1 / Fragment: UNP residues 1-30 and 106-185 / Mutation: RRF domain II deletion and GGG insertion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: frr, rrf, b0172, JW0167 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A805 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 14, 2004 |
Radiation | Monochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 343272 / Num. obs: 343272 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.3→3.36 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.398 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 1NKW Resolution: 3.33→8.13 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 117914.76 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.3143 Å2 / ksol: 0.118211 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.33→8.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.33→3.45 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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