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- PDB-7l4i: Crystal structure of a substrate-trapping variant of PPM1H phosphatase -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l4i | ||||||
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Title | Crystal structure of a substrate-trapping variant of 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 | ![]() | 328.1 KB | Display | ![]() |
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PDB format | ![]() | 265.5 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 ![]() 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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Components
#1: Protein | Mass: 50317.965 Da / Num. of mol.: 2 / Mutation: D288A, 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: 2.64 Å3/Da / Density % sol: 53.5 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / Details: 30% PEG 1500 |
-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: Sep 30, 2019 |
Radiation | Monochromator: 0.979279 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.58→28.97 Å / Num. obs: 34086 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 13.6 / Num. measured all: 224906 |
Reflection shell | Resolution: 2.58→2.7 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.651 / Num. unique obs: 3998 / CC1/2: 0.879 / Rpim(I) all: 0.272 / Rrim(I) all: 0.707 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6b67 Resolution: 2.58→28.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.08 / 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: 132.78 Å2 / Biso mean: 57.6578 Å2 / Biso min: 27.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.58→28.97 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: 16.9335 Å / Origin y: 60.984 Å / Origin z: 95.9169 Å
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Refinement TLS group |
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