+Open data
-Basic information
Entry | Database: PDB / ID: 8a8s | |||||||||
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Title | 30S ribosomal protein S24e from Thermococcus kodakarensis | |||||||||
Components | 30S ribosomal protein S24e | |||||||||
Keywords | GENE REGULATION / high pressure adaptation protein dynamics structural constituent of ribosome | |||||||||
Function / homology | Function and homology information ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation Similarity search - Function | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.659 Å | |||||||||
Authors | Calio, A. / Hoh, F. | |||||||||
Funding support | France, 2items
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Citation | Journal: To Be Published Title: 30S ribosomal protein S24e from Thermococcus kodakarensis Authors: Calio, A. / Hoh, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a8s.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a8s.ent.gz | 21.2 KB | Display | PDB format |
PDBx/mmJSON format | 8a8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a8s_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 8a8s_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | 8a8s_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 8a8s_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/8a8s ftp://data.pdbj.org/pub/pdb/validation_reports/a8/8a8s | HTTPS FTP |
-Related structure data
Related structure data | 2v94S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11199.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: rps24e, TK1696 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIY8 |
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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: 2.16 Å3/Da / Density % sol: 42.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0,1M sodium acetate pH 4,6 30% PEG 300 / PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.69 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.69 Å / Relative weight: 1 |
Reflection | Resolution: 1.659→37.1 Å / Num. obs: 9962 / % possible obs: 88 % / Redundancy: 1.6 % / CC1/2: 0.997 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.659→1.687 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 453 / CC1/2: 0.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V94 Resolution: 1.659→30.81 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 58.93 Å2 / Biso mean: 22.696 Å2 / Biso min: 9.7 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.659→30.81 Å
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