+Open data
-Basic information
Entry | Database: PDB / ID: 3bn0 | ||||||
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Title | The ribosomal protein S16 from Aquifex aeolicus | ||||||
Components | 30S ribosomal protein S16 | ||||||
Keywords | RIBOSOME / ribosomal protein / Ribonucleoprotein | ||||||
Function / homology | Function and homology information small ribosomal subunit / structural constituent of ribosome / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Pylypenko, O. / Rak, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Extreme temperature tolerance of a hyperthermophilic protein coupled to residual structure in the unfolded state Authors: Wallgren, M. / Aden, J. / Pylypenko, O. / Mikaelsson, T. / Johansson, L.B.-A. / Rak, A. / Wolf-Watz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bn0.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bn0.ent.gz | 23.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bn0_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 3bn0_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 3bn0_validation.xml.gz | 7 KB | Display | |
Data in CIF | 3bn0_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/3bn0 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/3bn0 | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13067.429 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpsP / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM 2 (DE3) / References: UniProt: O66523 |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 2000 MME, 100mM Tris pH 6-7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97919 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2→10 Å / Num. all: 9015 / Num. obs: 9015 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.041 / Net I/σ(I): 17.55 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.71 / Rsym value: 0.197 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.011 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 37.438 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.049 Å / Total num. of bins used: 20
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