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Yorodumi- PDB-4khp: Structure of the Thermus thermophilus 30S ribosomal subunit in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4khp | ||||||
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Title | Structure of the Thermus thermophilus 30S ribosomal subunit in complex with de-6-MSA-pactamycin | ||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / Pactamycin / 30S / mRNA / E site / tRNA / Ribosome / Translation / Antibiotic / RIBOSOME-ANTIBIOTIC complex / de-6-MSA-pactamycin and pactamycin analog | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Tourigny, D.S. / Fernandez, I.S. / Kelley, A.C. / Ramakrishnan, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Crystal Structure of a Bioactive Pactamycin Analog Bound to the 30S Ribosomal Subunit. Authors: Tourigny, D.S. / Fernandez, I.S. / Kelley, A.C. / Vakiti, R.R. / Chattopadhyay, A.K. / Dorich, S. / Hanessian, S. / Ramakrishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4khp.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4khp.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4khp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4khp_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 4khp_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 4khp_validation.xml.gz | 132.8 KB | Display | |
Data in CIF | 4khp_validation.cif.gz | 191.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/4khp ftp://data.pdbj.org/pub/pdb/validation_reports/kh/4khp | HTTPS FTP |
-Related structure data
Related structure data | 15jeS 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
-RNA chain , 2 types, 2 molecules AX
#1: RNA chain | Mass: 488986.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 |
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#22: RNA chain | Mass: 1790.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 |
-30S Ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU
#2: Protein | Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371 |
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#3: Protein | Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372 |
#4: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373 |
#5: Protein | Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5 |
#6: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8 |
#7: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291 |
#8: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS |
#9: Protein | Mass: 14298.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374 |
#10: Protein | Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7 |
#11: Protein | Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376 |
#12: Protein | Mass: 13875.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3 |
#13: Protein | Mass: 13623.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377 |
#14: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS |
#15: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76 |
#16: Protein | Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 |
#17: Protein | Mass: 11722.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS |
#18: Protein | Mass: 8155.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0 |
#19: Protein | Mass: 8949.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2 |
#20: Protein | Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3 |
-Non-polymers , 3 types, 111 molecules
#23: Chemical | ChemComp-PAR / #24: Chemical | ChemComp-PCY / | #25: Chemical | ChemComp-MG / |
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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: 4.64 Å3/Da / Density % sol: 73.48 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Mes-KOH (pH 6.5), 200 mM KCl, 75 mM NH4Cl, 15 mM MgCl2, and 26% (vol/vol) 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.99 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→29.7 Å / Num. all: 234683 / Num. obs: 234683 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.47 / Rsym value: 0.691 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 15JE Resolution: 3.1→29.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.359 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.129 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 306 Å2 / Biso mean: 83.2593 Å2 / Biso min: 11.56 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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