[English] 日本語
Yorodumi- PDB-4yhh: Crystal structure of the 30S ribosomal subunit from Thermus therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yhh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the 30S ribosomal subunit from Thermus thermophilus in complex with tigecycline | ||||||
Components |
| ||||||
Keywords | RIBOSOME / protein synthesis / antibiotic | ||||||
Function / homology | Function and homology information small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.417 Å | ||||||
Authors | Schedlbauer, A. / Kaminishi, T. / Ochoa-Lizarralde, B. / Dhimole, N. / Zhou, S. / Lopez-Alonso, J.P. / Connell, S.R. / Fucini, P. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yhh.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yhh.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4yhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/4yhh ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yhh | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zm6S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382 |
---|
-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) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371 |
---|---|
#3: Protein | Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372 |
#4: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373 |
#5: Protein | Mass: 17067.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / 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) / References: UniProt: Q5SLP8 |
#7: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / 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) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS |
#9: Protein | Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374 |
#10: Protein | Mass: 11398.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7 |
#11: Protein | Mass: 12161.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376 |
#12: Protein | Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3 |
#13: Protein | Mass: 13494.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377 |
#14: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS |
#15: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76 |
#16: Protein | Mass: 10152.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3 |
#17: Protein | Mass: 12194.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS |
#18: Protein | Mass: 8497.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0 |
#19: Protein | Mass: 9455.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2 |
#20: Protein | Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380 |
#21: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIH3 |
-Non-polymers , 3 types, 106 molecules
#22: Chemical | ChemComp-T1C / | ||
---|---|---|---|
#23: Chemical | ChemComp-MG / #24: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.88 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å |
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: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.417→48.716 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: resname T1C |