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Yorodumi- PDB-1zar: Crystal Structure of A.fulgidus Rio2 Kinase Complexed With ADP an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zar | ||||||
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Title | Crystal Structure of A.fulgidus Rio2 Kinase Complexed With ADP and Manganese Ions | ||||||
Components | Rio2 kinase | ||||||
Keywords | TRANSFERASE / serine kinase / winged-helix / RIO domain / ADP-Mn complex / rRNA processing | ||||||
Function / homology | Function and homology information non-specific serine/threonine protein kinase / phosphorylation / 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: 1.75 Å | ||||||
Authors | Laronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A. | ||||||
Citation | Journal: Febs J. / Year: 2005 Title: Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes. 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 | 1zar.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zar.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/1zar ftp://data.pdbj.org/pub/pdb/validation_reports/za/1zar | HTTPS FTP |
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-Related structure data
Related structure data | 1zaoC 1tqiS 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: 32857.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: Rio2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-pLysS-DE3 / References: UniProt: O30245 | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.68 Details: PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE , pH 3.68, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 / Wavelength: 0.99997 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 32601 / Num. obs: 32109 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.035 |
Reflection shell | Resolution: 1.75→1.795 Å / Redundancy: 3.7 % / Rsym value: 0.125 / % possible all: 87.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TQI Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.133 / SU ML: 0.071 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / 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: 25.235 Å2
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Refine analyze | Luzzati coordinate error obs: 0.117 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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