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Yorodumi- PDB-1lw3: Crystal Structure of Myotubularin-related protein 2 complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lw3 | ||||||
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Title | Crystal Structure of Myotubularin-related protein 2 complexed with phosphate | ||||||
Components | Myotubularin-related protein 2 | ||||||
Keywords | HYDROLASE / PROTEIN-PHOSPHATE COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of receptor catabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase / Synthesis of PIPs at the ER membrane / 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 receptor catabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase / Synthesis of PIPs at the ER membrane / 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 / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Begley, M.J. / Taylor, G.S. / Kim, S.-A. / Veine, D.M. / Dixon, J.E. / Stuckey, J.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lw3.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lw3.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lw3_validation.pdf.gz | 382 KB | Display | wwPDB validaton report |
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Full document | 1lw3_full_validation.pdf.gz | 395.3 KB | Display | |
Data in XML | 1lw3_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1lw3_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lw3 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lw3 | HTTPS FTP |
-Related structure data
Related structure data | 1m7rSC 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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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 75006.742 Da / Num. of mol.: 1 / Fragment: PH and phosphatase domains (residues 1-643) / Mutation: C417S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTMR2 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q13614, phosphatidylinositol-3-phosphatase | ||
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#2: Chemical | #3: 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: 1.91 Å3/Da / Density % sol: 35.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 35000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 20, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→30 Å / Num. obs: 25681 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.288 / % possible all: 73.8 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 27735 / % possible obs: 92 % / Num. measured all: 154888 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 73.8 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M7R Resolution: 2.3→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 409927.74 / Data cutoff high rms absF: 409927.74 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 69.33 Å2 / ksol: 0.5 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 8 Å / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.207 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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