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Yorodumi- PDB-1zth: Crystal Structure of A.fulgidus Rio1 serine protein kinase bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zth | ||||||
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Title | Crystal Structure of A.fulgidus Rio1 serine protein kinase bound to ADP and Manganese ion | ||||||
Components | Rio1 serine protein kinase | ||||||
Keywords | TRANSFERASE / protein Kinase / ribosome biogenesis / rRNA / ADP / manganese | ||||||
Function / homology | Function and homology information non-specific serine/threonine protein kinase / hydrolase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Wlodawer, A. / LaRonde-LeBlanc, N. | ||||||
Citation | Journal: Febs J. / Year: 2005 Title: Structure and activity of the atypical serine kinase Rio1. Authors: Laronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zth.cif.gz | 231.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zth.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zth_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1zth_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1zth_validation.xml.gz | 49 KB | Display | |
Data in CIF | 1zth_validation.cif.gz | 70.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/1zth ftp://data.pdbj.org/pub/pdb/validation_reports/zt/1zth | HTTPS FTP |
-Related structure data
Related structure data | 1zp9C 1ztfSC 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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Unit cell |
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-Components
#1: Protein | Mass: 30653.500 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: Rio1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: GenBank: 11499392, UniProt: O28471*PLUS #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ADP / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.33 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: PEG 4000, MES, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9686 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→30 Å / Num. all: 81701 / Num. obs: 78499 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.147 |
Reflection shell | Resolution: 1.89→1.939 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.35 / % possible all: 79.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZTF Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.807 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.175 / 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: 30.063 Å2
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Refine analyze | Luzzati coordinate error obs: 0.219 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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