+Open data
-Basic information
Entry | Database: PDB / ID: 1ztf | ||||||
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Title | Crystal Structure of A.fulgidus Rio1 serine protein kinase | ||||||
Components | Rio1 serine protein kinase | ||||||
Keywords | TRANSFERASE / protein Kinase / ribosome biogenesis / rRNA | ||||||
Function / homology | Function and homology information preribosome, small subunit precursor / maturation of SSU-rRNA / non-specific serine/threonine protein kinase / hydrolase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 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 | 1ztf.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ztf.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ztf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ztf_validation.pdf.gz | 741.2 KB | Display | wwPDB validaton report |
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Full document | 1ztf_full_validation.pdf.gz | 748.8 KB | Display | |
Data in XML | 1ztf_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1ztf_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/1ztf ftp://data.pdbj.org/pub/pdb/validation_reports/zt/1ztf | HTTPS FTP |
-Related 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: 30653.500 Da / Num. of mol.: 1 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 pLysS / References: GenBank: 11499392, UniProt: O28471*PLUS |
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#2: Chemical | ChemComp-XYA / |
#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: 2.35 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.3 Details: PEG 4000, MES, ammonuim sulfate, pH 6.3, 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: 0.9794, 0.9795, 1.0000 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 6, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.99→40 Å / Num. all: 18480 / Num. obs: 18215 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.99→39.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.15 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.173 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.304 Å2
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Refine analyze | Luzzati coordinate error obs: 0.214 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→39.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.042 Å / Total num. of bins used: 20
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