+Open data
-Basic information
Entry | Database: PDB / ID: 6g0j | ||||||
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Title | Inactive Fe-PP1 | ||||||
Components | Serine/threonine-protein phosphatase PP1-alpha catalytic subunit | ||||||
Keywords | HYDROLASE / Phosphatase / Iron / oxidative stress / cell cycle | ||||||
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 / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / response to lead ion / adherens junction / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Salvi, F. / Barabas, O. / Koehn, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: FEBS Lett. / Year: 2018 Title: Effects of stably incorporated iron on protein phosphatase-1 structure and activity. Authors: Salvi, F. / Trebacz, M. / Kokot, T. / Hoermann, B. / Rios, P. / Barabas, O. / Koehn, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g0j.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g0j.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 6g0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/6g0j ftp://data.pdbj.org/pub/pdb/validation_reports/g0/6g0j | HTTPS FTP |
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-Related structure data
Related structure data | 6g0iC 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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Unit cell |
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-Components
#1: Protein | Mass: 37647.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Two cysteine residues are modeled as oxidized / Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli) References: UniProt: P62136, protein-serine/threonine phosphatase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: 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: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 28% w/v PEG 3350, 0.1 M TRIS-Cl,pH 8.0 RT, 1 M Lithium Chloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.81 Å / Num. obs: 19896 / % possible obs: 97.3 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1662 / CC1/2: 0.806 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MOV Resolution: 2.1→46.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.442 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.181 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.462 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→46.81 Å
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Refine LS restraints |
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