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Yorodumi- PDB-2x7g: Structure of human serine-arginine-rich protein-specific kinase 2... -
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-Basic information
Entry | Database: PDB / ID: 2x7g | ||||||
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Title | Structure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B | ||||||
Components | UNCHARACTERIZED PROTEIN SRPK2 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MRNA SPLICING / PHOSPHOPROTEIN / MRNA PROCESSING / DIFFERENTIATION / NUCLEOTIDE-BINDING / SPLICEASOME ASSEMBLY / ATP COMPETITIVE INHIBITOR / KINASE / NUCLEUS / ATP-BINDING / SPLICE FACTOR TRAFFICKING | ||||||
Function / homology | Function and homology information nuclear speck organization / R-loop processing / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / positive regulation of viral genome replication / positive regulation of cell cycle / 14-3-3 protein binding ...nuclear speck organization / R-loop processing / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / positive regulation of viral genome replication / positive regulation of cell cycle / 14-3-3 protein binding / RNA splicing / positive regulation of neuron apoptotic process / peptidyl-serine phosphorylation / angiogenesis / cell differentiation / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / nucleolus / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Pike, A.C.W. / Savitsky, P. / Fedorov, O. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Pike, A.C.W. / Savitsky, P. / Fedorov, O. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Structure of Human Serine-Arginine-Rich Protein- Specific Kinase 2 (Srpk2) Bound to Purvalanol B Authors: Pike, A.C.W. / Savitsky, P. / Fedorov, O. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x7g.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x7g.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 2x7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x7g_validation.pdf.gz | 792.4 KB | Display | wwPDB validaton report |
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Full document | 2x7g_full_validation.pdf.gz | 794.8 KB | Display | |
Data in XML | 2x7g_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2x7g_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7g ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7g | HTTPS FTP |
-Related structure data
Related structure data | 1wbpS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44300.676 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 62-267,519-699 Source method: isolated from a genetically manipulated source Details: SYNTHETIC CONSTRUCT ENGINEERED TO REMOVE INTERVENING REGION. Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: C9JQJ0, UniProt: P78362*PLUS, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 126 molecules
#2: Chemical | ChemComp-PVB / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | SYNTHETIC CONSTRUCT WITH 268-518 REMOVED |
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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: 3.6 Å3/Da / Density % sol: 65.82 % / Description: NONE |
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Crystal grow | pH: 4.75 / Details: 0.5M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9796 |
Detector | Type: RAYONIX / Detector: CCD / Date: Sep 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.21 Å / Num. obs: 22306 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WBP Resolution: 2.5→45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.616 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.352 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45 Å
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