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Yorodumi- PDB-1bxy: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L30 FROM THERMUS THERMOPHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bxy | ||||||
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Title | CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L30 FROM THERMUS THERMOPHILUS AT 1.9 A RESOLUTION: CONFORMATIONAL FLEXIBILITY OF THE MOLECULE. | ||||||
Components | PROTEIN (RIBOSOMAL PROTEIN L30) | ||||||
Keywords | RIBOSOME / RIBOSOMAL PROTEIN / CONFORMATIONAL CHANGES | ||||||
Function / homology | Function and homology information cytosolic large ribosomal subunit / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fedorov, R. / Nevskaya, N. / Khairullina, A. / Tishchenko, S. / Mikhailov, A. / Garber, M. / Nikonov, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of ribosomal protein L30 from Thermus thermophilus at 1.9 A resolution: conformational flexibility of the molecule. Authors: Fedorov, R. / Nevskaya, N. / Khairullina, A. / Tishchenko, S. / Mikhailov, A. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bxy.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bxy.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bxy_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
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Full document | 1bxy_full_validation.pdf.gz | 419.1 KB | Display | |
Data in XML | 1bxy_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1bxy_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/1bxy ftp://data.pdbj.org/pub/pdb/validation_reports/bx/1bxy | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.5139, -0.7218, -0.4636), Vector: |
-Components
#1: Protein | Mass: 6799.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: VK1 / Description: CLONED GENE / Gene: RPL30 / Species (production host): Escherichia coli / Gene (production host): RPL30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P74909 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.04 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.5 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80 Å / Num. obs: 15544 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % |
Reflection | *PLUS Highest resolution: 1.85 Å / Num. obs: 35601 / % possible obs: 82.9 % / Num. measured all: 150778 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 92.7 % / Num. measured obs: 79.4 / Rmerge(I) obs: 0.319 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.6 Å2 |