+Open data
-Basic information
Entry | Database: PDB / ID: 4u20 | |||||||||
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Title | Crystal structure of the E. coli ribosome bound to flopristin. | |||||||||
Components |
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Keywords | RIBOSOME / Protein biosynthesis / RNA / transfer / exit / peptidyl / 30S / 70S / 16S / ribosomal subunit / antibiotic / streptogramin | |||||||||
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 / translation repressor activity / negative regulation of translational initiation / 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 / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / : / 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 small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / molecular adaptor activity / rRNA binding / 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. MDS42 (bacteria) Escherichia coli (E. coli) Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | |||||||||
Model details | This structure consists of multiple PDB entries | |||||||||
Authors | Noeske, J. / Huang, J. / Olivier, N.B. / Giacobbe, R.A. / Zambrowski, M. / Cate, J.H.D. | |||||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2014 Title: Synergy of streptogramin antibiotics occurs independently of their effects on translation. Authors: Noeske, J. / Huang, J. / Olivier, N.B. / Giacobbe, R.A. / Zambrowski, M. / Cate, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u20.cif.gz | 7.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4u20.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4u20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/4u20 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/4u20 | HTTPS FTP |
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-Related structure data
Related structure data | 4u1uC 4u1vC 4u24C 4u25C 4u26C 4u27C C: citing same article (ref.) |
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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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Details | There are 2 biological units in the assymetric unit. |
-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. MDS42 (bacteria) References: GenBank: 359330873 #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. MDS42 (bacteria) References: GenBank: 359330873 #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. MDS42 (bacteria) References: GenBank: 359330873 |
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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, 2225 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | #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: 3.4 Å3/Da / Density % sol: 63.7 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 / Details: PEG8k, MPD |
-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 | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→70 Å / Num. obs: 1094024 / % possible obs: 87.4 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 48.88 Å2 / Rmerge F obs: 0.989 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.157 / Χ2: 0.969 / Net I/σ(I): 4.39 / Num. measured all: 2259195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.9→69.327 Å / FOM work R set: 0.76 / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.86 / Stereochemistry target values: ML Details: THE ELECTRON DENSITY MAPS OF THE FIRST RIBOSOME ARE BETTER THAN THOSE OF THE SECOND RIBOSOME IN THE ASYMMETRIC UNIT. THEREFORE, SUBUNIT AND ANTIBIOTIC COORDINATES OF THE FIRST RIBOSOME ...Details: THE ELECTRON DENSITY MAPS OF THE FIRST RIBOSOME ARE BETTER THAN THOSE OF THE SECOND RIBOSOME IN THE ASYMMETRIC UNIT. THEREFORE, SUBUNIT AND ANTIBIOTIC COORDINATES OF THE FIRST RIBOSOME (CHAINS START WITH A AND B) ARE OF BETTER QUALITY THAN THOSE OF THE SECOND RIBOSOME (CHAINS START WITH C AND D).
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 205.8 Å2 / Biso mean: 61.58 Å2 / Biso min: 2.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→69.327 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
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