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Open data
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Basic information
Entry | Database: PDB / ID: 7l4j | ||||||
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Title | Crystal structure of WT PPM1H phosphatase | ||||||
![]() | Protein phosphatase 1H | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 331.4 KB | Display | ![]() |
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PDB format | ![]() | 267.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kprC ![]() 7l4iC ![]() 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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Components
#1: Protein | Mass: 50361.977 Da / Num. of mol.: 2 / Mutation: C56A 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: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion / Details: 0.1M imidazole 20% jeffamine ED-2001 / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.45→28.97 Å / Num. obs: 74295 / % possible obs: 99.1 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.781 / Num. unique obs: 3324 / CC1/2: 0.779 / Rpim(I) all: 0.321 / Rrim(I) all: 0.855 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6b67 Resolution: 2.451→28.966 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 26.86 / 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: 123.47 Å2 / Biso mean: 60.4708 Å2 / Biso min: 29.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.451→28.966 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -17.5354 Å / Origin y: 10.7873 Å / Origin z: -21.3942 Å
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Refinement TLS group |
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