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Yorodumi- PDB-5d8h: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d8h | |||||||||
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Title | CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON | |||||||||
Components |
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Keywords | RIBOSOMAL PROTEIN / ribosome / P-stalk / archaea / ANTIBIOTIC / THIOSTREPTON | |||||||||
Function / homology | Function and homology information large ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / defense response to bacterium / translation / extracellular region Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) Streptomyces azureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | |||||||||
Authors | Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B. | |||||||||
Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON Authors: Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8h.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8h.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 5d8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d8h_validation.pdf.gz | 501.1 KB | Display | wwPDB validaton report |
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Full document | 5d8h_full_validation.pdf.gz | 522.2 KB | Display | |
Data in XML | 5d8h_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 5d8h_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8h ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8h | 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
-50S ribosomal protein ... , 2 types, 2 molecules BC
#2: Protein | Mass: 23635.162 Da / Num. of mol.: 1 / Fragment: UNP residues 9-221 / Mutation: Met changed to SeMet Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: rpl10, rplP0, MJ0509 / Plasmid: pET-11c/MjaP0NTF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54049 |
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#3: Protein | Mass: 17794.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: rpl11, MJ0373 / Plasmid: pET-11c/MjaL11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54030 |
-RNA chain / Protein/peptide , 2 types, 2 molecules AD
-Non-polymers , 4 types, 83 molecules
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-NA / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 mM Tris-HCl, pH 7.5, 10% PEG 8000, 20% glycerol, 1 mM TCEP (tris(2-carboxyethyl)phosphine), 0.125 mM CTAB |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97953 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 50260 / Num. obs: 50260 / % possible obs: 99.3 % / Redundancy: 3.47 % / Rsym value: 0.061 / Net I/σ(I): 14.96 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.32 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→45.545 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 30.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.545 Å
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Refine LS restraints |
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LS refinement shell |
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