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- PDB-1m7r: Crystal Structure of Myotubularin-related Protein-2 (MTMR2) Compl... -

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Basic information

Entry
Database: PDB / ID: 1m7r
TitleCrystal Structure of Myotubularin-related Protein-2 (MTMR2) Complexed with Phosphate
ComponentsMyotubularin-related Protein-2
KeywordsHYDROLASE / 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 / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / regulation of phosphatidylinositol dephosphorylation / myelin assembly / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the late endosome membrane / positive regulation of early endosome to late endosome transport / 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-3,5-bisphosphate 3-phosphatase activity / regulation of phosphatidylinositol dephosphorylation / myelin assembly / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the late endosome membrane / positive regulation of early endosome to late endosome transport / Synthesis of PIPs at the early endosome membrane / negative regulation of myelination / phosphatidylinositol dephosphorylation / negative regulation of excitatory postsynaptic potential / negative regulation of endocytosis / phosphatidylinositol biosynthetic process / negative regulation of receptor internalization / dendritic spine maintenance / vacuolar membrane / 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 / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Myotubularin-like, phosphatase domain / Myotubularin family / Myotubularin-like phosphatase domain / Myotubularin phosphatase domain. / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Protein-tyrosine phosphatase, catalytic ...Myotubularin-like, phosphatase domain / Myotubularin family / Myotubularin-like phosphatase domain / Myotubularin phosphatase domain. / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsBegley, M.J. / Taylor, G.S. / Kim, S.-A. / Veine, D.M. / Dixon, J.E. / Stuckey, J.A.
CitationJournal: 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
DepositionJul 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Category: pdbx_unobs_or_zero_occ_residues
Revision 1.4Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_residues ...database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myotubularin-related Protein-2
B: Myotubularin-related Protein-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3936
Polymers150,0132
Non-polymers3804
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.25, 82.66, 100.13
Angle α, β, γ (deg.)90.00, 117.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Myotubularin-related Protein-2


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.) 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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 0.968 Å3/Da / Density % sol: 31.93 %
Crystal growMethod: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.0 mg/mlprotein1drop
27 mMTris-HCl1droppH8.0
315 mM1dropNaCl
42 mMdithiothreitol1drop
5100 mMHEPES1reservoirpH7.5
62 mMTCEP1reservoir
710 mM1reservoirCaCl2-2H2O
82.75 %PEG350001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2001 / Details: Mirrors
RadiationMonochromator: SI 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3332 10 %Random
Rwork0.207 ---
all-33991 --
obs-33351 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.2692 Å2 / ksol: 0.455054 e/Å3
Displacement parametersBiso mean: 41.51 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å23.94 Å2
2--1.32 Å20 Å2
3----3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8380 0 20 235 8635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.87
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 505 9.3 %
Rwork0.341 4905 -
obs-5410 95.6 %
Xplor fileSerial 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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.87

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