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- PDB-5gnh: Myotubularin-related protein 2 -

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Basic information

Entry
Database: PDB / ID: 5gnh
TitleMyotubularin-related protein 2
ComponentsMyotubularin-related protein 2
KeywordsHYDROLASE / MTMR2 / PI / Myotubularin-related protein
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
PHOSPHATE ION / Phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, B.I. / Bong, S.M.
CitationJournal: To Be Published
Title: Crystal structure of MTMR2
Authors: Lee, B.I. / Bong, S.M.
History
DepositionJul 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)132,3475
Polymers132,0622
Non-polymers2853
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-29 kcal/mol
Surface area40490 Å2
2
A: Myotubularin-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1262
Polymers66,0311
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21310 Å2
MethodPISA
3
B: Myotubularin-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2213
Polymers66,0311
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.344, 82.820, 99.972
Angle α, β, γ (deg.)90.00, 117.59, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / Auth seq-ID: 75 - 586 / Label seq-ID: 3 - 514

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Myotubularin-related protein 2 / Phosphatidylinositol-3 / 5-bisphosphate 3-phosphatase / Phosphatidylinositol-3-phosphate phosphatase


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 ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES pH 7.5, 10% (v/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33545 / % possible obs: 95.3 % / Redundancy: 4.7 % / Net I/σ(I): 15.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1721 5.1 %RANDOM
Rwork0.20295 ---
obs0.20574 31823 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.843 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8283 0 15 32 8330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198515
X-RAY DIFFRACTIONr_bond_other_d0.0040.028001
X-RAY DIFFRACTIONr_angle_refined_deg1.461.94711539
X-RAY DIFFRACTIONr_angle_other_deg1.12318376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8851008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85723.176425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.949151450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4921570
X-RAY DIFFRACTIONr_chiral_restr0.0870.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219552
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022094
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6885.2744044
X-RAY DIFFRACTIONr_mcbond_other3.675.2734043
X-RAY DIFFRACTIONr_mcangle_it5.9847.8995048
X-RAY DIFFRACTIONr_mcangle_other5.9847.95049
X-RAY DIFFRACTIONr_scbond_it3.5335.5054471
X-RAY DIFFRACTIONr_scbond_other3.5335.514460
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.818.1336474
X-RAY DIFFRACTIONr_long_range_B_refined8.57540.129314
X-RAY DIFFRACTIONr_long_range_B_other8.57540.1269311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 65668 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.604→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 118 -
Rwork0.308 2095 -
obs--85.41 %

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