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Yorodumi- PDB-1tqm: Crystal Structure of A. fulgidus Rio2 Serine Protein Kinase Bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tqm | ||||||
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Title | Crystal Structure of A. fulgidus Rio2 Serine Protein Kinase Bound to AMPPNP | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | RIBOSOME / SERINE KINASE / AMPPNP / ANP | ||||||
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: 1.99 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 | 1tqm.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tqm.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tqm ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tqm | HTTPS FTP |
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-Related structure data
Related structure data | 1tqiSC 1tqpC 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 on special symmetry positions |
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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) / 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-ANP / |
#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: 2.57 Å3/Da / Density % sol: 51.67 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99998 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 21, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→29 Å / Num. all: 21420 / Num. obs: 20313 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.042 / Net I/σ(I): 40.9 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 12.1 / Rsym value: 0.125 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1tqi Resolution: 1.99→28.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.353 / SU ML: 0.097 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.16 / 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: 23.56 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.99→28.99 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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