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- PDB-7kpr: Structure of wild-type PPM1H phosphatase at 3.1 Angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kpr | ||||||
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Title | Structure of wild-type PPM1H phosphatase at 3.1 Angstrom resolution | ||||||
![]() | Protein phosphatase 1H | ||||||
![]() | HYDROLASE / Rab GTPase / membrane trafficking / PPM family | ||||||
Function / homology | ![]() [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / glutamatergic synapse / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khan, A.R. / Waschbusch, D. | ||||||
![]() | ![]() Title: Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. Authors: Waschbusch, D. / Berndsen, K. / Lis, P. / Knebel, A. / Lam, Y.P. / Alessi, D.R. / Khan, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 370.3 KB | Display | ![]() |
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PDB format | ![]() | 269.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 458.6 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l4iC ![]() 7l4jC ![]() 7n0zC ![]() 6b67S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.381201247254, -0.73465906491, 0.561214457617), (-0.727955782525, -0.612731068418, -0.307637800805), (0.569882433297, -0.291267396289, -0.768373161997)Vector: 7. ...NCS oper: (Code: given Matrix: (0.381201247254, -0.73465906491, 0.561214457617), Vector: |
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Components
#1: Protein | Mass: 53890.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9ULR3, protein-serine/threonine phosphatase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 6.5 / Details: 10% isopropanol, 5% PEG4000, 0.05M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→28.78 Å / Num. obs: 19927 / % possible obs: 99.25 % / Redundancy: 6.7 % / Biso Wilson estimate: 92.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Net I/σ(I): 19.83 |
Reflection shell | Resolution: 3.09→3.2 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 1853 / CC1/2: 0.855 / Rrim(I) all: 0.84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6b67 Resolution: 3.09→28.78 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 26.0137 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 98.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→28.78 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.765726149409 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.8518424065 Å / Origin y: 10.743001406 Å / Origin z: 21.1718562482 Å
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Refinement TLS group | Selection details: all |