+Open data
-Basic information
Entry | Database: PDB / ID: 4yy3 | ||||||
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Title | 30S ribosomal subunit- HigB complex | ||||||
Components |
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Keywords | RIBOSOME / Bacterial toxins / Stringent response / translational control / RNase | ||||||
Function / homology | Function and homology information plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding ...plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / Hydrolases; Acting on ester bonds / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / negative regulation of cell population proliferation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Proteus vulgaris (bacteria) Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Schureck, M.A. / Maehigashi, T. / Dunham, C.M. | ||||||
Citation | Journal: Rna / Year: 2016 Title: mRNA bound to the 30S subunit is a HigB toxin substrate. Authors: Schureck, M.A. / Maehigashi, T. / Miles, S.J. / Marquez, J. / Dunham, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yy3.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4yy3.ent.gz | 2.1 MB | Display | PDB format |
PDBx/mmJSON format | 4yy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yy3_validation.pdf.gz | 694.9 KB | Display | wwPDB validaton report |
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Full document | 4yy3_full_validation.pdf.gz | 982.3 KB | Display | |
Data in XML | 4yy3_validation.xml.gz | 158.1 KB | Display | |
Data in CIF | 4yy3_validation.cif.gz | 223.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/4yy3 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yy3 | HTTPS FTP |
-Related structure data
Related structure data | 1j5eS 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
-30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 |
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#3: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372 |
#4: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373 |
#5: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5 |
#6: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8 |
#7: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291 |
#8: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS |
#9: Protein | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374 |
#10: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7 |
#11: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376 |
#12: Protein | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3 |
#13: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377 |
#14: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS |
#15: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76 |
#16: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3 |
#17: Protein | Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS |
#18: Protein | Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0 |
#19: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2 |
#20: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380 |
#21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3 |
-RNA chain / Protein , 2 types, 2 molecules AY
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382 |
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#22: Protein | Mass: 13713.409 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higB / Plasmid: pBAD/Myc-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): BW25113 / References: UniProt: Q7A225 |
-Non-polymers , 2 types, 196 molecules
#23: Chemical | ChemComp-MG / #24: Chemical | |
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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: 4.49 Å3/Da / Density % sol: 72.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14% MPD, 0.2 M KCL , 75 mM NH4Cl, 15 mM MgCl2 , 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2012 / Details: MIRRORS |
Radiation | Monochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 163739 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 109.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J5E Resolution: 3.6→46.158 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→46.158 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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