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Yorodumi- PDB-4gyg: Crystal structure of the Rio2 kinase from Chaetomium thermophilum -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gyg | ||||||
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Title | Crystal structure of the Rio2 kinase from Chaetomium thermophilum | ||||||
Components | Rio2 kinase | ||||||
Keywords | TRANSFERASE / RIO-type ser/thr protein kinase / Ribosome biogenesis factor / pre-40S maturation / ribosomal RNA processing / pre-40S / ribosomal RNA / phosphorylation | ||||||
Function / homology | Function and homology information non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.482 Å | ||||||
Authors | Ferreira-Cerca, S. / Sagar, V. / Schafer, T. / Diop, M. / Wesseling, A.M. / Lu, H. / Chai, E. / Hurt, E. / LaRonde-LeBlanc, N. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit. Authors: Ferreira-Cerca, S. / Sagar, V. / Schafer, T. / Diop, M. / Wesseling, A.M. / Lu, H. / Chai, E. / Hurt, E. / Laronde-Leblanc, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gyg.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gyg.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/4gyg ftp://data.pdbj.org/pub/pdb/validation_reports/gy/4gyg | HTTPS FTP |
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-Related structure data
Related structure data | 4gyiC 1tqpS 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: 44691.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033330, Rio2 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(TM) PLysS / References: UniProt: G0S5R3 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE AS PROVIDED, INCLUDING RESIDUES 1-23 IS THE CORRECT SEQUENCE OF THE PROTEIN. THE ...THE SEQUENCE AS PROVIDED, INCLUDING RESIDUES 1-23 IS THE CORRECT SEQUENCE OF THE PROTEIN. THE UNIPROT DATABASE HAVE BEEN NOTIFIED OF THE ERROR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, 16% Poly-Ethylene Glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2011 |
Radiation | Monochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→33.9 Å / Num. all: 12932 / Num. obs: 12674 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 51.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.82→2.96 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.071 / Rsym value: 0.163 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TQP Resolution: 2.482→33.89 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 1.96 / Phase error: 27.32 / 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 mean: 56.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.482→33.89 Å
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Refine LS restraints |
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LS refinement shell |
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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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