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- PDB-1zsq: Crystal Structure of MTMR2 in complex with phosphatidylinositol 3... -

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Basic information

Entry
Database: PDB / ID: 1zsq
TitleCrystal Structure of MTMR2 in complex with phosphatidylinositol 3-phosphate
ComponentsMyotubularin-related protein 2
KeywordsHYDROLASE / Protein-Phospholipid Complex
Function / homology
Function and homology information


negative regulation of receptor catabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase / regulation of phosphatidylinositol dephosphorylation / Synthesis of PIPs at the ER membrane / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / myelin assembly / phosphatidylinositol-3-phosphate phosphatase activity / positive regulation of early endosome to late endosome transport / 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 / regulation of phosphatidylinositol dephosphorylation / Synthesis of PIPs at the ER membrane / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / myelin assembly / phosphatidylinositol-3-phosphate phosphatase activity / positive regulation of early endosome to late endosome transport / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / negative regulation of myelination / negative regulation of excitatory postsynaptic potential / phosphatidylinositol dephosphorylation / 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 / cytosol / cytoplasm
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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-PIB / Phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBegley, M.J. / Taylor, G.S. / Brock, M.A. / Ghosh, P. / Woods, V.L. / Dixon, J.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Molecular basis for substrate recognition by MTMR2, a myotubularin family phosphoinositide phosphatase
Authors: Begley, M.J. / Taylor, G.S. / Brock, M.A. / Ghosh, P. / Woods, V.L. / Dixon, J.E.
History
DepositionMay 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 20, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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 2.1Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myotubularin-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9076
Polymers61,1041
Non-polymers8035
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.227, 66.227, 261.678
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1239-

HOH

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Components

#1: Protein Myotubularin-related protein 2


Mass: 61104.402 Da / Num. of mol.: 1 / Fragment: PH-GRAM and Phosphatase Domains / Mutation: C417S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTMR2, KIAA1073 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13614, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PIB / 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE / D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO


Mass: 554.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O16P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.352 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 35000, Tris, TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2004 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 52572 / Num. obs: 52572 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 28.5 Å2 / Rsym value: 0.102 / Net I/σ(I): 21.9
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4449 / Rsym value: 0.452 / % possible all: 85

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LW3

1lw3


Resolution: 1.82→50 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4858 -random
Rwork0.218 ---
all-48397 --
obs-48397 90.2 %-
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-8 Å20 Å20 Å2
2--8 Å20 Å2
3----15.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 51 399 4636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d2.66
LS refinement shellResolution: 1.82→1.89 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.356 372 -
Rwork0.346 --
obs-3260 69.2 %

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