+Open data
-Basic information
Entry | Database: PDB / ID: 1q8z | ||||||
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Title | The apoenzyme structure of the yeast SR protein kinase, Sky1p | ||||||
Components | SR Protein Kinase | ||||||
Keywords | TRANSFERASE / disallowed / 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 / 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: 2.35 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 | 1q8z.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8z.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 1q8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q8z_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 1q8z_full_validation.pdf.gz | 493.3 KB | Display | |
Data in XML | 1q8z_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 1q8z_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8z ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8z | HTTPS FTP |
-Related structure data
Related structure data | 1q8yC 1q97C 1q99C 1howS 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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2 |
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Unit cell |
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-Components
#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 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.55 Å3/Da / Density % sol: 51.76 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 4.5 Details: 1.5M (NH4)2SO4, 100mM Na Acetate pH 4.5, 15% Ethylene Glycol. Crystals then dialyzed into 30% PEG 400 and 100mM Na Acetate pH 4.5, hanging drop, crystals soaked into low salt buffer, 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: Jun 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. all: 37306 / Num. obs: 34172 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.35→2.43 Å / % possible all: 85.6 |
Reflection | *PLUS Num. measured all: 198041 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 85.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.39 |
-Processing
Software |
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Refinement | Starting model: PDB code 1HOW Resolution: 2.35→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 28641 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |