+Open data
-Basic information
Entry | Database: PDB / ID: 6obu | |||||||||
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Title | PP1 Y134K in complex with Microcystin LR | |||||||||
Components |
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Keywords | HYDROLASE/TOXIN / phosphatase / HYDROLASE-TOXIN complex | |||||||||
Function / homology | Function and homology information regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Microcystis aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Choy, M.S. / Moon, T.M. / Bray, J.A. / Archuleta, T.L. / Shi, W. / Peti, W. / Page, R. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: SDS22 selectively recognizes and traps metal-deficient inactive PP1. Authors: Choy, M.S. / Moon, T.M. / Ravindran, R. / Bray, J.A. / Robinson, L.C. / Archuleta, T.L. / Shi, W. / Peti, W. / Tatchell, K. / Page, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6obu.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6obu.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 6obu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/6obu ftp://data.pdbj.org/pub/pdb/validation_reports/ob/6obu | HTTPS FTP |
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-Related structure data
Related structure data | 6obnC 6obpC 6obqC 6obrC 6obsC 4movS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 34128.156 Da / Num. of mol.: 2 / Fragment: UNP residues 7-300 / Mutation: Y134K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli) References: UniProt: P62136, protein-serine/threonine phosphatase #2: Protein/peptide | |
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-Non-polymers , 5 types, 355 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-CL / | #7: 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: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG6000, 1 M lithium chloride, 0.1 M MES, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40.17 Å / Num. obs: 49637 / % possible obs: 97.3 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.925 / Num. unique obs: 2812 / CC1/2: 0.553 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MOV Resolution: 1.95→40.17 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→40.17 Å
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Refine LS restraints |
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LS refinement shell |
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