+Open data
-Basic information
Entry | Database: PDB / ID: 4wf1 | |||||||||
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Title | Crystal structure of the E. coli ribosome bound to negamycin. | |||||||||
Components |
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Keywords | Ribosome/Antibiotic / Protein biosynthesis / ribosomes / RNA / transfer / exit / peptidyl / 30S / 70S / 16S / ribosomal subunit / antibiotic / streptogramin / Ribosome-Antibiotic 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 / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / 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 str. K-12 substr. MG1655 (bacteria) Escherichia coli (E. coli) Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.09 Å | |||||||||
Authors | Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. ...Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. / Miller, M.D. / Prince, D.B. / Cate, J.H.D. / Buurman, E.T. / Blanchard, S.C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome. Authors: Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. / Miller, M.D. / Prince, D.B. / Cate, J.H. / Buurman, ...Authors: Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. / Miller, M.D. / Prince, D.B. / Cate, J.H. / Buurman, E.T. / Blanchard, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wf1.cif.gz | 7.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4wf1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4wf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wf1 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wf1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 498725.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria) References: GenBank: 545778205 #22: RNA chain | Mass: 941306.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria) References: GenBank: 409785 #23: RNA chain | Mass: 38483.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria) References: GenBank: 545778205 |
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-30S ribosomal protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 24253.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V0 #3: Protein | Mass: 23078.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V3 #4: Protein | Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V8 #5: Protein | Mass: 15804.282 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7W1 #6: Protein | Mass: 11669.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02358 #7: Protein | Mass: 16861.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02359 #8: Protein | Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7W7 #9: Protein | Mass: 14554.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7X3 #10: Protein | Mass: 11196.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R5 #11: Protein | Mass: 12487.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R9 #12: Protein | Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S3 #13: Protein | Mass: 12625.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S9 #14: Protein | Mass: 11475.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG59 #15: Protein | Mass: 10159.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ADZ4 #16: Protein | Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7T3 #17: Protein | Mass: 9263.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG63 #18: Protein | Mass: 6466.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7T7 #19: Protein | Mass: 9057.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U3 #20: Protein | Mass: 9506.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U7 #21: Protein | Mass: 6067.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P68679 |
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+50S ribosomal protein ... , 30 types, 59 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...
-Non-polymers , 4 types, 2221 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | ChemComp-NEG / | #57: 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: 3.38 Å3/Da / Density % sol: 63.59 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 / Details: PEG8k, MPD |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3.09→41.14 Å / Num. obs: 1043787 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 72.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.058 / Net I/σ(I): 14.9 / Num. measured all: 6209734 / Scaling rejects: 444 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 3.09→41.136 Å / FOM work R set: 0.841 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 23.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 228.16 Å2 / Biso mean: 67.48 Å2 / Biso min: 1.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.09→41.136 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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