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Yorodumi- PDB-3wxm: Crystal structure of archaeal Pelota and GTP-bound EF1 alpha complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wxm | |||||||||
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Title | Crystal structure of archaeal Pelota and GTP-bound EF1 alpha complex | |||||||||
Components |
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Keywords | TRANSLATION/HYDROLASE / mRNA surveillance / Ribosome / TRANSLATION-HYDROLASE complex | |||||||||
Function / homology | Function and homology information RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / translation elongation factor activity / endonuclease activity / Hydrolases; Acting on ester bonds / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Aeropyrum pernix K1 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | |||||||||
Authors | Kobayashi, K. / Ishitani, R. / Nureki, O. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1 alpha complex Authors: Kobayashi, K. / Kikuno, I. / Kuroha, K. / Saito, K. / Ito, K. / Ishitani, R. / Inada, T. / Nureki, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wxm.cif.gz | 640 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wxm.ent.gz | 516.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/3wxm ftp://data.pdbj.org/pub/pdb/validation_reports/wx/3wxm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49662.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: tuf, APE_1844 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus / References: UniProt: Q9YAV0 #2: Protein | Mass: 41470.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: pelA, APE_1800.1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus References: UniProt: Q9YAZ5, Hydrolases; Acting on ester bonds #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.2M NaCl, 100mM imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 216696 / % possible obs: 95.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 38.36 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→32.433 Å / FOM work R set: 0.793 / SU ML: 0.41 / σ(F): 1.48 / Phase error: 28.2 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.52 Å2 / Biso mean: 45.73 Å2 / Biso min: 15.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→32.433 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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