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Yorodumi- PDB-4n3n: Crystal structure of eukaryotic translation initiation factor eIF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n3n | |||||||||
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Title | Crystal structure of eukaryotic translation initiation factor eIF5B (517-1116) from Chaetomium thermophilum, apo form | |||||||||
Components | Eukaryotic translation initiation factor 5B-like protein, eIF5B(517-C) | |||||||||
Keywords | TRANSLATION / Translation initiation / GTPase / eIF5B/IF2 / Subunit joining / Ribosome | |||||||||
Function / homology | Function and homology information protein-synthesizing GTPase / translation initiation factor activity / GTPase activity / GTP binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.752 Å | |||||||||
Authors | Kuhle, B. / Ficner, R. | |||||||||
Citation | Journal: Embo J. / Year: 2014 Title: eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining. Authors: Kuhle, B. / Ficner, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n3n.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n3n.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 4n3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n3n_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 4n3n_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 4n3n_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4n3n_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/4n3n ftp://data.pdbj.org/pub/pdb/validation_reports/n3/4n3n | HTTPS FTP |
-Related structure data
Related structure data | 4n3gC 4n3sC 4ncfC 4nclC 4ncnC 1g7rS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 67239.531 Da / Num. of mol.: 1 / Fragment: unp residues 517-1092 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029840 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S8G9 |
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#2: Chemical | ChemComp-LAC / |
#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: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 12% PEG 20000, 10 mM Na-lactate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82658 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.82658 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→35.68 Å / Num. obs: 21910 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 77.16 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1G7R Resolution: 2.752→35.683 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7751 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 28.45 / 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: 156.58 Å2 / Biso mean: 64.6618 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.752→35.683 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: 8 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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