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Yorodumi- PDB-5yv5: Crystal structure of the complex of archaeal ribosomal stalk prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yv5 | ||||||
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Title | Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal ribosome recycling factor aABCE1. | ||||||
Components |
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Keywords | TRANSLATION / Ribosome recycling / Ribosomal stalk / Complex | ||||||
Function / homology | Function and homology information translational elongation / ribosome / structural constituent of ribosome / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus COM1 (archaea) Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Imai, H. / Abe, T. / Miyoshi, T. / Nishikawa, S. / Ito, K. / Uchiumi, T. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: The ribosomal stalk protein is crucial for the action of the conserved ATPase ABCE1 Authors: Imai, H. / Abe, T. / Miyoshi, T. / Nishikawa, S.I. / Ito, K. / Uchiumi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yv5.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yv5.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 5yv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yv5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5yv5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5yv5_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 5yv5_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/5yv5 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yv5 | HTTPS FTP |
-Related structure data
Related structure data | 1yqtS S: Starting model for refinement |
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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
#1: Protein | Mass: 60483.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_02505 / Production host: Escherichia coli (E. coli) / References: UniProt: I6V0C7 | ||||
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#2: Protein/peptide | Mass: 1879.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZJ7*PLUS | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15% (w/v) PEG 4000, 10% (v/v) 2-propanol, 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.98 Å / Num. obs: 31682 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Redundancy: 3.18 % / Net I/σ(I): 21.03 |
Reflection shell | Resolution: 2.1→2.22 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YQT Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.942 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.331 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→19.98 Å
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Refine LS restraints |
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