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Yorodumi- PDB-3r3t: Crystal Structure of 30S Ribosomal Protein S from Bacillus anthracis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r3t | ||||||
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Title | Crystal Structure of 30S Ribosomal Protein S from Bacillus anthracis | ||||||
Components | 30S ribosomal protein S6 | ||||||
Keywords | RNA BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / beta-barrel / cytosol | ||||||
Function / homology | Function and homology information rRNA binding / ribosome / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 30S Ribosomal Protein S from Bacillus anthracis Authors: Kim, Y. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r3t.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r3t.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 3r3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r3t_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 3r3t_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 3r3t_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3r3t_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r3t ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r3t | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11697.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS5327, BA_5723, GBAA_5723, rpsF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81JI2 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM magnesium chloride, 0.1 M HEPES, 30 % v/v polyethylene glycol monomethyl ether 550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 10636 / Num. obs: 10636 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 51.15 Å2 / Rsym value: 0.105 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 4.65 / Num. unique all: 511 / Rsym value: 0.621 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.302→45.609 Å / Isotropic thermal model: mixed / Cross valid method: throughput / σ(F): 0 / Phase error: 25.5 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.712 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.302→45.609 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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