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- PDB-1lw3: Crystal Structure of Myotubularin-related protein 2 complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1lw3
TitleCrystal Structure of Myotubularin-related protein 2 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-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
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
PHOSPHATE ION / Myotubularin-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMay 30, 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Feb 14, 2024Group: 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)75,2924
Polymers75,0071
Non-polymers2853
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.080, 66.080, 261.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological unit is a monomer

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Components

#1: Protein Myotubularin-related protein 2


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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 274 / 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: 1.91 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.0 mg/mlprotein1drop
27 mMTris-HCl1droppH8.0
315 mM1dropNaCl
42 mMdithiothreitol1drop
53.0 %PEG350001reservoir
6100 mMHEPES1reservoirpH7.5
72 mMdithiothreitol1reservoir

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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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M7R

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 2298 10 %random
Rwork0.2087 ---
all0.25 26109 --
obs0.25 23283 89.2 %-
Solvent computationSolvent model: flat model / Bsol: 69.33 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 45.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.33 Å20 Å20 Å2
2--9.33 Å20 Å2
3----18.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 15 274 4478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.35515
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.3-2.440.3329221100.276927220.02219370.9
2.4-2.520.37192390.2722588
2.52-2.680.31272800.24032773
2.68-2.880.33882900.25072867
2.88-3.150.28322850.22472981
3.15-3.570.31913100.23013177
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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