+Open data
-Basic information
Entry | Database: PDB / ID: 4iyl | |||||||||
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Title | 30S ribosomal protein S15 from Campylobacter jejuni | |||||||||
Components | 30S ribosomal protein S15 | |||||||||
Keywords | RIBOSOMAL PROTEIN / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / rRNA binding / translation / NIAID / National Institute of Allergy and Infectious Diseases | |||||||||
Function / homology | Function and homology information cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | |||||||||
Biological species | Campylobacter jejuni subsp. jejuni (Campylobacter) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | |||||||||
Authors | Osipiuk, J. / Nocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: To be Published Title: 30S ribosomal protein S15 from Campylobacter jejuni Authors: Osipiuk, J. / Nocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iyl.cif.gz | 29.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iyl.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 4iyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iyl_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 4iyl_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 4iyl_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 4iyl_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/4iyl ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iyl | HTTPS FTP |
-Related structure data
Related structure data | 2y0y S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | biological unit is the same as asymmetric unit, based on ribosome structure |
-Components
#1: Protein | Mass: 10519.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0884, rpsO / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PA13 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.49 M sodium phosphate, 0.91 M di-potassium phosphate, pH 7.1, 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: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→32.3 Å / Num. all: 5992 / Num. obs: 5992 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.39 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y0Y 2y0y Resolution: 2.36→32.27 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.575 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.287 / ESU R Free: 0.237 / 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: 151.27 Å2 / Biso mean: 81.4788 Å2 / Biso min: 45.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→32.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.362→2.423 Å / Total num. of bins used: 20
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