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Yorodumi- PDB-1pkp: THE STRUCTURE OF RIBOSOMAL PROTEIN S5 REVEALS SITES OF INTERACTIO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pkp | ||||||
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Title | THE STRUCTURE OF RIBOSOMAL PROTEIN S5 REVEALS SITES OF INTERACTION WITH 16S RRNA | ||||||
Components | RIBOSOMAL PROTEIN S5 | ||||||
Keywords | RIBOSOMAL PROTEIN | ||||||
Function / homology | Function and homology information small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Ramakrishnan, V. / White, S.W. | ||||||
Citation | Journal: Nature / Year: 1992 Title: The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Authors: Ramakrishnan, V. / White, S.W. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Model for the Three-Dimensional Folding of 16S Ribosomal RNA Authors: Stern, S. / Weiser, B. / Noller, H.F. #2: Journal: FEBS Lett. / Year: 1983 Title: Proteins of the Bacillus Stearothermophilus Ribosome: A 5A Structure Analysis of Protein S5 Authors: White, S.W. / Appelt, K. / Dijk, J. / Wilson, K.S. #3: Journal: J.Biol.Chem. / Year: 1983 Title: Proteins of the Bacillus Stearothermophilus Ribosome. Crystallization of Proteins L30 and S5 Authors: Appelt, K. / White, S.W. / Wilson, K.S. #4: Journal: Mol.Gen.Genet. / Year: 1975 Title: Effect of Different Mutations in Ribosomal Protein S5 of Escherichia Coli on Translational Fidelity Authors: Piepersberg, W. / Bock, A. / Wittmann, H.-G. #5: Journal: Mol.Gen.Genet. / Year: 1975 Title: Genetic Position and Amino Acid Replacements of Several Mutations in Ribosomal Protein S5 from Escherichia Coli Authors: Piepersberg, W. / Bock, A. / Yaguchi, M. / Wittmann, H.-G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pkp.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pkp.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1pkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pkp_validation.pdf.gz | 362.4 KB | Display | wwPDB validaton report |
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Full document | 1pkp_full_validation.pdf.gz | 367.4 KB | Display | |
Data in XML | 1pkp_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 1pkp_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/1pkp ftp://data.pdbj.org/pub/pdb/validation_reports/pk/1pkp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15914.577 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: BACILLUS STEAROTHERMOPHILUS / Gene (production host): BACILLUS STEAROTHERMOPHILUS / References: UniProt: P02357 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.86 % | ||||||||||||||||||
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Crystal grow | *PLUS Method: unknown / PH range low: 8.2 / PH range high: 7.2 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 5829 / Num. measured all: 14806 / Rmerge(I) obs: 0.051 |
-Processing
Software |
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Refinement | Resolution: 2.8→6 Å / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor all: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.74 |