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Yorodumi- PDB-5wnl: Crystal structure of murine receptor-interacting protein 4 (Ripk4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wnl | ||||||
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Title | Crystal structure of murine receptor-interacting protein 4 (Ripk4) D143N bound to staurosporine | ||||||
Components | Receptor-interacting serine/threonine-protein kinase 4 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information morphogenesis of an epithelium / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Huang, C.S. / Hymowitz, S.G. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Crystal Structure of Ripk4 Reveals Dimerization-Dependent Kinase Activity. Authors: Huang, C.S. / Oberbeck, N. / Hsiao, Y.C. / Liu, P. / Johnson, A.R. / Dixit, V.M. / Hymowitz, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wnl.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wnl.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/5wnl ftp://data.pdbj.org/pub/pdb/validation_reports/wn/5wnl | 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
#1: Protein | Mass: 38988.039 Da / Num. of mol.: 1 / Fragment: residues 1-342 / Mutation: D143N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk4, Ankrd3, Pkk / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9ERK0, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-STU / |
#3: Chemical | ChemComp-CL / |
#4: 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: 3.6 Å3/Da / Density % sol: 65.87 % |
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Crystal grow | Temperature: 292 K / Method: microbatch Details: 0.1M HEPES pH 7.5, 200 mM magnesium chloride, 10% isopropanol, 15% ethylene glycol, and 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 37451 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.835 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.219 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.086 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→30 Å
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Refine LS restraints |
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