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- PDB-7qfb: Crystal structure of Protein Phosphatase 1 in complex with PP1-bi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qfb | ||||||
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Title | Crystal structure of Protein Phosphatase 1 in complex with PP1-binding peptide from PTG | ||||||
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![]() | HYDROLASE / phosphatase | ||||||
Function / homology | ![]() glycogen binding / protein phosphatase type 1 complex / 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 ...glycogen binding / protein phosphatase type 1 complex / 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 / glycogen biosynthetic process / regulation of translational initiation / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / protein phosphatase binding / dendritic spine / molecular adaptor activity / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Semrau, M.S. / Storici, P. / Lolli, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular architecture of the glycogen- committed PP1/PTG holoenzyme. Authors: Semrau, M.S. / Giachin, G. / Covaceuszach, S. / Cassetta, A. / Demitri, N. / Storici, P. / Lolli, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148 KB | Display | ![]() |
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PDB format | ![]() | 114.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.4 KB | Display | ![]() |
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Full document | ![]() | 457 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qf7C ![]() 7qfaC ![]() 7qm2C ![]() 6zegS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 34162.148 Da / Num. of mol.: 1 / Fragment: phosphatase domain (residues 7-300) Mutation: First residue GHMGS derive from the expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P62136, protein-serine/threonine phosphatase |
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#2: Protein/peptide | Mass: 2963.407 Da / Num. of mol.: 1 / Fragment: peptide 81-107 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 176 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % / Mosaicity: 0.08 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Lithium sulfate, 1.4 M sodium malonate / PH range: 6 to 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→68.34 Å / Num. obs: 35005 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.053 / Rrim(I) all: 0.202 / Net I/σ(I): 10 / Num. measured all: 499594 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZEG Resolution: 2.05→59.89 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.91 Å2 / Biso mean: 38.6283 Å2 / Biso min: 17.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→59.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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