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- PDB-4v4h: Crystal structure of the bacterial ribosome from Escherichia coli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v4h | |||||||||
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Title | Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution. | |||||||||
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![]() | RIBOSOME / KASUGAMYCIN | |||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded 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 / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schuwirth, B.S. / Vila-Sanjurjo, A. / Cate, J.H.D. | |||||||||
![]() | ![]() Title: Structural analysis of kasugamycin inhibition of translation. Authors: Schuwirth, B.S. / Day, J.M. / Hau, C.W. / Janssen, G.R. / Dahlberg, A.E. / Cate, J.H.D. / Vila-Sanjurjo, A. | |||||||||
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, 1VS5, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 1VS5, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND ARE DEPOSITED UNDER: 70S RIBOSOME ONE: 1VS5 (30S SUBUNIT), 1VS6 (50S SUBUNIT) 70S RIBOSOME TWO: 1VS7 (30S SUBUNIT), 1VS8 (50S SUBUNIT) | |||||||||
Remark 600 | HETEROGEN MO4 38 HAS SQUARE-PLANAR HYDRATION OF MG2+ MO4 10,16,30,31,34,40,43,44,51 HAVE 2 VICINAL ...HETEROGEN MO4 38 HAS SQUARE-PLANAR HYDRATION OF MG2+ MO4 10,16,30,31,34,40,43,44,51 HAVE 2 VICINAL WATERS MISSING FROM HYDRATION OF MG2+ MO3 11,48 HAVE ALL WATER BONDS MUTUALLY ORTHOGONAL TO OTHER MG2+-WATER BONDS MO3 4,9 HAVE ALL WATERS AND MG2+ IN-PLANE MO2 35 HAS ALL WATERS AND MG2+ ORTHOGONAL |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 6.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 866.2 KB | Display | |
Data in CIF | ![]() | 1.2 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pns ![]() 1pnu S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() ![]() #22: RNA chain | Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #23: RNA chain | Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules ACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCPAQCQ...
#2: Protein | Mass: 26031.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 23514.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 17629.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 20055.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 14146.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 14886.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 13870.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 13768.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 13128.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 11606.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 10319.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 9724.491 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 9005.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 10455.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 9708.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 26781.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | Mass: 8524.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+50S RIBOSOMAL PROTEIN ... , 29 types, 58 molecules BVDVBCDCBDDDBEDEBFDFBGDGBHDHBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...
-Non-polymers , 3 types, 1972 molecules ![](data/chem/img/KSG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#53: Chemical | #54: Chemical | ChemComp-MG / #55: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS-HCL, EDTA, PH 7.5, BATCH, TEMPERATURE 277K, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.46→70 Å / Num. obs: 693093 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.46→3.55 Å / Redundancy: 0 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / % possible all: 87.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1PNS, 1PNU Resolution: 3.46→70 Å / Isotropic thermal model: GROUPED BY RESIDUE / σ(F): 0 / Stereochemistry target values: TORSIONAL DYNAMICS
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Displacement parameters | Biso mean: 58.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.46→70 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.46→3.48 Å
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