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- PDB-4yhh: Crystal structure of the 30S ribosomal subunit from Thermus therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yhh | ||||||
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Title | Crystal structure of the 30S ribosomal subunit from Thermus thermophilus in complex with tigecycline | ||||||
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![]() | RIBOSOME / protein synthesis / antibiotic | ||||||
Function / homology | ![]() ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schedlbauer, A. / Kaminishi, T. / Ochoa-Lizarralde, B. / Dhimole, N. / Zhou, S. / Lopez-Alonso, J.P. / Connell, S.R. / Fucini, P. | ||||||
![]() | ![]() Title: Structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome. Authors: Schedlbauer, A. / Kaminishi, T. / Ochoa-Lizarralde, B. / Dhimole, N. / Zhou, S. / Lopez-Alonso, J.P. / Connell, S.R. / Fucini, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 888 KB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 153.7 KB | Display | |
Data in CIF | ![]() | 215.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zm6S 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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Unit cell |
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Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 489348.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#2: Protein | Mass: 26159.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 17067.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 11398.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 12161.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 13494.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 10152.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 12194.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 8497.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 9455.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 3 types, 106 molecules ![](data/chem/img/T1C.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
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#22: Chemical | ChemComp-T1C / | ||
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#23: Chemical | ChemComp-MG / #24: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: HEPES-KOH, MgCl2, NH4Cl, beta-mercaptoethanol, MPD, spermidine |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 192315 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.162 / Net I/σ(I): 4.45 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 6.995 / Mean I/σ(I) obs: 0.3 / % possible all: 84.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2ZM6 Resolution: 3.417→48.716 Å / FOM work R set: 0.611 / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 103.251 Å2 / ksol: 0.231 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 476.6 Å2 / Biso mean: 212.93 Å2 / Biso min: 42.71 Å2
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Refinement step | Cycle: final / Resolution: 3.417→48.716 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 3.4 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 306.8429 Å / Origin y: 179.115 Å / Origin z: 33.1229 Å
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Refinement TLS group | Selection details: resname T1C |