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- PDB-6srr: Crystal structure of human SHIP2 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 6srr
TitleCrystal structure of human SHIP2 catalytic domain
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
KeywordsHYDROLASE
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 / 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. ...Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / 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
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: 2.45 Å
AuthorsWhitfield, H. / Brearley, C.A. / Hemmings, A.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Allosteric Site on SHIP2 Identified Through Fluorescent Ligand Screening and Crystallography: A Potential New Target for Intervention.
Authors: Whitfield, H. / Hemmings, A.M. / Mills, S.J. / Baker, K. / White, G. / Rushworth, S. / Riley, A.M. / Potter, B.V.L. / Brearley, C.A.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,4882
Polymers72,4882
Non-polymers00
Water59433
1
B: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2


Theoretical massNumber of molelcules
Total (without water)36,2441
Polymers36,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2


Theoretical massNumber of molelcules
Total (without water)36,2441
Polymers36,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.130, 62.120, 115.620
Angle α, β, γ (deg.)90.000, 92.380, 90.000
Int Tables number4
Space group name H-MP1211

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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: 36243.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Production host: Escherichia coli (E. coli)
References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Sodium citrate, 20 % w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.45→42.3 Å / Num. obs: 23610 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 59.79 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.052 / Rrim(I) all: 0.109 / Net I/σ(I): 9.5 / Num. measured all: 103280
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.514.41756917330.5050.5411.1411.799.8
10.96-42.33.80.05710622760.9970.0320.06524.296

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A9C

4a9c


Resolution: 2.45→36.491 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.9
RfactorNum. reflection% reflection
Rfree0.2371 1112 4.71 %
Rwork0.1865 --
obs0.1889 23587 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 189.25 Å2 / Biso mean: 80.2604 Å2 / Biso min: 32.54 Å2
Refinement stepCycle: final / Resolution: 2.45→36.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 0 33 4831
Biso mean---63.16 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094921
X-RAY DIFFRACTIONf_angle_d0.9946689
X-RAY DIFFRACTIONf_chiral_restr0.06740
X-RAY DIFFRACTIONf_plane_restr0.008854
X-RAY DIFFRACTIONf_dihedral_angle_d17.2322877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.56150.35591670.28252764100
2.5615-2.69650.38841220.2822280199
2.6965-2.86540.2871460.2428277699
2.8654-3.08650.30891300.209280299
3.0865-3.39690.27781520.21322808100
3.3969-3.8880.24591190.17862835100
3.888-4.89660.18421420.1553280999
4.8966-36.490.20121340.1675288099
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)
15.35990.84880.07973.72280.64784.2710.03830.54-0.5165-0.15230.27-0.30350.35170.286-0.27050.43120.0449-0.04010.4935-0.15170.4446-4.1167-28.9179-49.8797
22.454-0.8128-0.72536.1933-1.73373.7894-0.0872-0.19020.1004-0.6771-0.0930.7102-0.1957-0.80860.20150.55120.0325-0.10.7391-0.11920.5294-16.9569-16.1708-51.3848
33.15951.73811.34582.85551.5222.17460.1303-0.1745-0.02110.1239-0.0447-0.15080.00730.0875-0.08980.4072-0.00350.01140.6075-0.0750.4065-3.9684-14.7634-38.1792
43.3230.23360.39465.89633.49925.4595-0.0946-0.48420.43420.2630.4634-0.434-0.62240.786-0.25810.5572-0.04150.03380.5923-0.17480.5618-18.45214.919-11.2138
59.0057-1.21721.65493.18571.02784.81980.23940.0271-0.46650.09240.4482-0.52710.08470.9318-0.57280.4240.00490.03290.5349-0.16940.5026-18.1484-1.2323-26.8483
66.76580.72260.40476.08923.19655.4963-0.2777-0.57810.40040.35560.2881-0.0252-0.01640.13370.09150.38910.04340.03680.4162-0.05170.3851-23.72365.3673-17.4978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 421 through 550 )B421 - 550
2X-RAY DIFFRACTION2chain 'B' and (resid 551 through 600 )B551 - 600
3X-RAY DIFFRACTION3chain 'B' and (resid 601 through 731 )B601 - 731
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 615 )A422 - 615
5X-RAY DIFFRACTION5chain 'A' and (resid 616 through 652 )A616 - 652
6X-RAY DIFFRACTION6chain 'A' and (resid 653 through 730 )A653 - 730

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