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- PDB-5okp: Crystal structure of human SHIP2 Phosphatase-C2 double mutant F59... -

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Basic information

Entry
Database: PDB / ID: 5okp
TitleCrystal structure of human SHIP2 Phosphatase-C2 double mutant F593D/L597D
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
KeywordsHYDROLASE / SHIP2 / Phosphatase / C2 / phosphatidylinositol (3 / 4 / 5)-triphosphate
Function / homology
Function and homology information


negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / ruffle assembly / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process ...negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / ruffle assembly / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process / Synthesis of IP3 and IP4 in the cytosol / establishment of mitotic spindle orientation / Synthesis of PIPs at the plasma membrane / regulation of immune response / Interleukin receptor SHC signaling / ERK1 and ERK2 cascade / SH2 domain binding / basal plasma membrane / post-embryonic development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / filopodium / actin filament organization / response to insulin / SH3 domain binding / spindle pole / endocytosis / glucose metabolic process / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of protein localization / lamellipodium / actin binding / gene expression / cell adhesion / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / Golgi apparatus / nucleus / cytosol
Similarity search - Function
Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLe Coq, J. / Lietha, D.
CitationJournal: Elife / Year: 2017
Title: Structural basis for interdomain communication in SHIP2 providing high phosphatase activity.
Authors: Le Coq, J. / Camacho-Artacho, M. / Velazquez, J.V. / Santiveri, C.M. / Gallego, L.H. / Campos-Olivas, R. / Dolker, N. / Lietha, D.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9695
Polymers52,7201
Non-polymers2484
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint10 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.745, 73.426, 157.964
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-1123-

HOH

21A-1136-

HOH

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Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing ...Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C / SH2 domain-containing inositol 5'-phosphatase 2 / SHIP-2


Mass: 52720.344 Da / Num. of mol.: 1 / Mutation: F593D, L597D
Source method: isolated from a genetically manipulated source
Details: The first two residues are from the expression vector in which the gene was cloned.
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pOPINJ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2(DE3)pLysS
References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 50 mM HEPES pH 7.1, 17.5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→78.98 Å / Num. obs: 40283 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Net I/σ(I): 11.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.768 / Rpim(I) all: 0.372 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→78.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.945 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20469 2118 5 %RANDOM
Rwork0.17787 ---
obs0.17923 40283 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.11 Å2
2---0.68 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.85→78.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 16 139 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193516
X-RAY DIFFRACTIONr_bond_other_d0.0030.023218
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9494757
X-RAY DIFFRACTIONr_angle_other_deg0.88337473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73624.012167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21815610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7711521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
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_it0.8682.0511692
X-RAY DIFFRACTIONr_mcbond_other0.8682.051691
X-RAY DIFFRACTIONr_mcangle_it1.5243.0582107
X-RAY DIFFRACTIONr_mcangle_other1.5233.0592108
X-RAY DIFFRACTIONr_scbond_it0.9732.2221823
X-RAY DIFFRACTIONr_scbond_other0.9722.2221823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6233.2672646
X-RAY DIFFRACTIONr_long_range_B_refined3.81823.3543747
X-RAY DIFFRACTIONr_long_range_B_other3.75323.1593728
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 147 -
Rwork0.24 2993 -
obs--99.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81940.0156-0.00110.96050.09830.35-0.02210.0053-0.00390.00450.01090.05920.0204-0.02460.01120.00450.00420.01770.0657-0.00260.13710.113316.389641.3534
23.28381.6273-0.30225.61440.15762.39610.0141-0.08030.13730.7980.1392-0.016-0.0532-0.041-0.15330.1610.0470.02220.12930.00320.0492-22.782513.805965.9312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 731
2X-RAY DIFFRACTION2A746 - 874

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