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Yorodumi- PDB-1tqp: Crystal Structure of A. fulgidus Rio2 Serine Protein Kinase Bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tqp | ||||||
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Title | Crystal Structure of A. fulgidus Rio2 Serine Protein Kinase Bound to ATP | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | RIBOSOME / SERINE KINASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | LaRonde-LeBlanc, N. / Wlodawer, A. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structure of A. fulgidus Rio2 Defines a New Family of Serine Protein Kinases Authors: LaRonde-LeBlanc, N. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tqp.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tqp.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tqp ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tqp | HTTPS FTP |
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-Related structure data
Related structure data | 1tqiSC 1tqmC S: Starting model for refinement C: citing same article (ref.) |
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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: 33139.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: RIO2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-pLysS / References: UniProt: O30245 |
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#2: Chemical | ChemComp-ATP / |
#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: 2.59 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.83 Details: PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE, pH 3.83, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.7 Å / Num. all: 18666 / Num. obs: 18666 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.052 / Net I/σ(I): 26.78 |
Reflection shell | Resolution: 2.1→2.155 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 9.17 / Rsym value: 0.174 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1TQI Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.074 / SU ML: 0.11 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.17 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.01 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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