[English] 日本語
![](img/lk-miru.gif)
- PDB-1m7r: Crystal Structure of Myotubularin-related Protein-2 (MTMR2) Compl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1m7r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Myotubularin-related Protein-2 (MTMR2) Complexed with Phosphate | ||||||
![]() | Myotubularin-related Protein-2 | ||||||
![]() | HYDROLASE / Protein-phosphate complex | ||||||
Function / homology | ![]() negative regulation of receptor catabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-3-phosphatase / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / myelin assembly / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane ...negative regulation of receptor catabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-3-phosphatase / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / myelin assembly / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / positive regulation of early endosome to late endosome transport / negative regulation of myelination / negative regulation of excitatory postsynaptic potential / protein tyrosine/serine/threonine phosphatase activity / phosphatidylinositol dephosphorylation / negative regulation of endocytosis / phosphatidylinositol biosynthetic process / negative regulation of receptor internalization / vacuolar membrane / dendritic spine maintenance / Synthesis of PIPs at the plasma membrane / neuron development / protein dephosphorylation / synaptic membrane / synaptic vesicle / early endosome membrane / dendritic spine / postsynaptic density / axon / intracellular membrane-bounded organelle / dendrite / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Begley, M.J. / Taylor, G.S. / Kim, S.-A. / Veine, D.M. / Dixon, J.E. / Stuckey, J.A. | ||||||
![]() | ![]() Title: Crystal structure of a phosphoinositide phosphatase, MTMR2: insights into myotubular myopathy and Charcot-Marie-Tooth syndrome Authors: Begley, M.J. / Taylor, G.S. / Kim, S.-A. / Veine, D.M. / Dixon, J.E. / Stuckey, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 224.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 177.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 469.4 KB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 75006.742 Da / Num. of mol.: 2 / Fragment: PH and Phosphatase Domains (Residues 1-643) / Mutation: C417S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13614, phosphatidylinositol-3-phosphatase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 0.968 Å3/Da / Density % sol: 31.93 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 35000, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 20, 2001 / Details: Mirrors |
Radiation | Monochromator: SI 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 39438 / Num. obs: 39438 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 40.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.6→2.76 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.282 / % possible all: 95.6 |
Reflection | *PLUS Num. measured all: 459390 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.254 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2692 Å2 / ksol: 0.455054 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.51 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.212 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|