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Yorodumi- PDB-1q8y: The structure of the yeast SR protein kinase, Sky1p, with bound ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q8y | ||||||
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Title | The structure of the yeast SR protein kinase, Sky1p, with bound ADP | ||||||
Components | SR protein kinase | ||||||
Keywords | TRANSFERASE / protein kinase | ||||||
Function / homology | Function and homology information intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / cytoplasmic stress granule / positive regulation of protein import into nucleus / non-specific serine/threonine protein kinase ...intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / cytoplasmic stress granule / positive regulation of protein import into nucleus / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å | ||||||
Authors | Nolen, B. / Ngo, J. / Chakrabarti, S. / Vu, D. / Adams, J.A. / Ghosh, G. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Nucleotide-Induced Conformational Changes in the Saccharomyces cerevisiae SR Protein Kinase, Sky1p, Revealed by X-Ray Crystallography Authors: Nolen, B. / Ngo, J. / Chakrabarti, S. / Vu, D. / Adams, J.A. / Ghosh, G. | ||||||
History |
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Remark 999 | SEQUENCE 137 amino acids truncated from N-terminus, RESIDUES 305-538 WERE DELETED AND REPLACED WITH VAL-ASP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q8y.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8y.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8y ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43025.066 Da / Num. of mol.: 2 / Fragment: Sky1pdeltaN(137)deltaS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SKY1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLyS References: UniProt: Q03656, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 5 types, 273 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-ADE / | #6: Water | ChemComp-HOH / | |
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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: 2.47 Å3/Da / Density % sol: 50.11 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.5M (NH4)2SO4, 100mM NaAcetate pH 4.5, 15% Ethylene Glycol. Crystals then dialyzed into 30% PEG 400 and 100mM NaAcetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Nolen, B., (2001) Nat.Struct.Biol., 8, 176. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.54 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→39.84 Å / Num. all: 54358 / Num. obs: 53312 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.7 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 65 / Limit l min: 0 / Observed criterion F max: 291752.06 / Observed criterion F min: 1.049 |
Reflection shell | Resolution: 2.05→2.15 Å / % possible all: 93.7 |
Reflection | *PLUS Num. obs: 50520 / Num. measured all: 298198 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Resolution: 2.05→19.92 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 44.9792 Å2 / ksol: 0.372062 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 84.01 Å2 / Biso mean: 27.08 Å2 / Biso min: 9.42 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.14 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 37868 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2446 / Rfactor Rwork: 0.2102 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.26 |