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Yorodumi- PDB-4v54: Crystal structure of the bacterial ribosome from Escherichia coli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v54 | |||||||||
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Title | Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). | |||||||||
Components |
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Keywords | RIBOSOME / RNA-protein complex | |||||||||
Function / homology | Function and homology information stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / : / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Borovinskaya, M.A. / Pai, R.D. / Zhang, W. / Schuwirth, B.-S. / Holton, J.M. / Hirokawa, G. / Kaji, H. / Kaji, A. / Cate, J.H.D. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Authors: Borovinskaya, M.A. / Pai, R.D. / Zhang, W. / Schuwirth, B.S. / Holton, J.M. / Hirokawa, G. / Kaji, H. / Kaji, A. / Cate, J.H. | |||||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL UNIT CONSISTS OF TWO SUBUNITS. THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT. | |||||||||
Remark 400 | COMPOUND THIS FILE, 2QBD, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 2QBD, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND IS DEPOSITED UNDER: 70S RIBOSOME ONE: 2QBD (30S SUBUNIT), 2QBE (50S SUBUNIT) 70S RIBOSOME TWO: 2QBF (30S SUBUNIT), 2QBG (50S SUBUNIT) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v54.cif.gz | 6.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v54.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v54 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v54 | HTTPS FTP |
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-Related structure data
Related structure data | 4v52C 4v53C 4v55C 4v5yC 2avy 2aw4 2aw7 2awb 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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2 |
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Unit cell |
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-Components
-RNA chain , 3 types, 6 molecules AACABADABBDB
#1: RNA chain | Mass: 499690.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 83754040 #22: RNA chain | Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357928 #23: RNA chain | Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357927 |
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-30S ribosomal protein ... , 20 types, 40 molecules ACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCPAQCQ...
#2: Protein | Mass: 25900.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V3 #3: Protein | Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V8 #4: Protein | Mass: 17498.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1 #5: Protein | Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02358 #6: Protein | Mass: 19923.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02359 #7: Protein | Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W7 #8: Protein | Mass: 14755.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7X3 #9: Protein | Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R5 #10: Protein | Mass: 13739.778 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R9 #11: Protein | Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3 #12: Protein | Mass: 12997.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S9 #13: Protein | Mass: 11475.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG59 #14: Protein | Mass: 10290.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADZ4 #15: Protein | Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T3 #16: Protein | Mass: 9593.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG63 #17: Protein | Mass: 8874.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T7 #18: Protein | Mass: 10324.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U3 #19: Protein | Mass: 9577.268 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U7 #20: Protein | Mass: 26650.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V0 #21: Protein | Mass: 8392.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68679 |
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+50S ribosomal protein ... , 29 types, 58 molecules BIDIBCDCBDDDBKDKBPDPBEDEBYDYB0D0B4D4B1D1B3D3BVDVB2D2BLDLBMDM...
-Protein , 1 types, 2 molecules B6D6
#53: Protein | Mass: 21029.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q9WX76 |
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-Non-polymers , 3 types, 1972 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 14 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 63.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 7.5 Details: MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.111 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.111 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→123 Å / Num. obs: 738833 / % possible obs: 88 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3.3→3.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3 / % possible all: 52.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AVY, 2AW4, 2AW7, 2AWB Resolution: 3.3→40 Å / Isotropic thermal model: grouped by residue / σ(F): 0 / Stereochemistry target values: torsional dynamics
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Displacement parameters | Biso mean: 78.273 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→40 Å
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Refine LS restraints |
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