+Open data
-Basic information
Entry | Database: PDB / ID: 5gnh | ||||||
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Title | Myotubularin-related protein 2 | ||||||
Components | Myotubularin-related protein 2 | ||||||
Keywords | HYDROLASE / MTMR2 / PI / Myotubularin-related protein | ||||||
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 / 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 / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lee, B.I. / Bong, S.M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of MTMR2 Authors: Lee, B.I. / Bong, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gnh.cif.gz | 218 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gnh.ent.gz | 172.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/5gnh ftp://data.pdbj.org/pub/pdb/validation_reports/gn/5gnh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 75 - 586 / Label seq-ID: 3 - 514
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-Components
#1: Protein | Mass: 66031.086 Da / Num. of mol.: 2 / Fragment: UNP residues 73-643 / Mutation: C417S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTMR2, KIAA1073 / Production host: Escherichia coli (E. coli) References: UniProt: Q13614, phosphatidylinositol-3,5-bisphosphate 3-phosphatase, phosphatidylinositol-3-phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100mM HEPES pH 7.5, 10% (v/v) polyethylene glycol 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 33545 / % possible obs: 95.3 % / Redundancy: 4.7 % / Net I/σ(I): 15.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / SU B: 14.354 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.843 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→50 Å
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Refine LS restraints |
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