+Open data
-Basic information
Entry | Database: PDB / ID: 5m3q | ||||||
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Title | Crystal structure of Tif6 from Chaetomium thermophilum | ||||||
Components | Eukaryotic translation initiation factor 6 | ||||||
Keywords | RIBOSOME / Ribosome biogenesis / anti-association factor | ||||||
Function / homology | Function and homology information ribosomal subunit export from nucleus / ribosomal large subunit binding / ribosomal large subunit biogenesis / translation initiation factor activity / cytosolic ribosome assembly / nucleolus / cytoplasm Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Ahmed, Y.L. / Calvino, F.R. / Sinning, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Protein Sci. / Year: 2017 Title: Interaction network of the ribosome assembly machinery from a eukaryotic thermophile. Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. ...Authors: Baler, J. / Ahmed, Y.L. / Kallas, M. / Kornprobst, M. / Calvino, F.R. / Gnadig, M. / Thoms, M. / Stier, G. / Ismail, S. / Kharde, S. / Castillo, N. / Griesel, S. / Bastuck, S. / Bradatsch, B. / Thomson, E. / Flemming, D. / Sinning, I. / Hurt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m3q.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3q.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3q ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3q | HTTPS FTP |
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-Related structure data
Related structure data | 5m43C 1g62S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27441.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Gene: TIF6, CTHT_0025830 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S683 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Na-citrate pH 5.6 0.5 M Ammonium sulfate 1 M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2012 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→44.72 Å / Num. obs: 43931 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.031 / Rrim(I) all: 0.07 / Net I/σ(I): 16.8 / Num. measured all: 212576 / Scaling rejects: 49 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.531
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G62 Resolution: 1.5→41.256 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.73 / 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: 85.75 Å2 / Biso mean: 19.6297 Å2 / Biso min: 6.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→41.256 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: 16
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Refinement TLS params. | Method: refined / Origin x: -7.0998 Å / Origin y: 14.1623 Å / Origin z: 7.4883 Å
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Refinement TLS group |
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