[English] 日本語
Yorodumi- PDB-1q99: Crystal structure of the Saccharomyces cerevisiae SR protein kins... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q99 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Saccharomyces cerevisiae SR protein kinsae, Sky1p, complexed with the non-hydrolyzable ATP analogue, AMP-PNP | ||||||
Components | SR protein kinsae | ||||||
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 / intracellular signal transduction / 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: 2.11 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 |
| ||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q99.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q99.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 1q99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q99_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1q99_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1q99_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 1q99_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q99 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q99 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43025.066 Da / Num. of mol.: 2 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 |
---|
-Non-polymers , 6 types, 248 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.5 M (NH4)2SO4, 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
|
-Data collection
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: 2.11→40.11 Å / Num. all: 51095 / Num. obs: 49258 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 330018.77 / Observed criterion F min: 1.049 |
Reflection shell | Resolution: 2.11→2.18 Å / % possible all: 86.6 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 49644 / % possible obs: 96.5 % / Num. measured all: 280589 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS Rmerge(I) obs: 46.7 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.11→19.95 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 53.0035 Å2 / ksol: 0.39012 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 81.86 Å2 / Biso mean: 31.8 Å2 / Biso min: 7.81 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→19.95 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.11→2.2 Å / Rfactor Rfree error: 0.02
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Num. reflection obs: 41455 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2601 / Rfactor Rwork: 0.2201 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|