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- PDB-8pdi: The phosphatase and C2 domains of SHIP1 with covalent Z1763271112 -

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Basic information

Entry
Database: PDB / ID: 8pdi
TitleThe phosphatase and C2 domains of SHIP1 with covalent Z1763271112
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / ligand / phoshphatase / C2
Function / homology
Function and homology information


inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / negative regulation of monocyte differentiation ...inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / negative regulation of monocyte differentiation / phosphatidylinositol dephosphorylation / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of bone resorption / positive regulation of B cell differentiation / negative regulation of B cell proliferation / Synthesis of IP3 and IP4 in the cytosol / negative regulation of osteoclast differentiation / Synthesis of PIPs at the plasma membrane / PECAM1 interactions / negative regulation of interleukin-6 production / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / regulation of immune response / negative regulation of signal transduction / positive regulation of erythrocyte differentiation / determination of adult lifespan / SH3 domain binding / Signaling by CSF1 (M-CSF) in myeloid cells / Downstream TCR signaling / T cell receptor signaling pathway / cytoskeleton / intracellular signal transduction / positive regulation of apoptotic process / membrane raft / apoptotic process / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SHIP1/2 second C2 domain / SHIP1/2 first C2 domain / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Endonuclease/exonuclease/phosphatase superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
(5-phenyl-1,3,4-thiadiazol-2-yl)methanimine / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBradshaw, W.J. / Moreira, T. / Pascoa, T.C. / Bountra, C. / Chalk, R. / von Delft, F. / Brennan, P.E. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 United States
CitationJournal: Structure / Year: 2024
Title: Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2.
Authors: Bradshaw, W.J. / Kennedy, E.C. / Moreira, T. / Smith, L.A. / Chalk, R. / Katis, V.L. / Benesch, J.L.P. / Brennan, P.E. / Murphy, E.J. / Gileadi, O.
History
DepositionJun 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3015
Polymers52,8781
Non-polymers4244
Water9,584532
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint10 kcal/mol
Surface area20380 Å2
Unit cell
Length a, b, c (Å)62.498, 78.993, 89.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 / Inositol polyphosphate-5-phosphatase D / Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 ...Inositol polyphosphate-5-phosphatase D / Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 / Phosphatidylinositol 4 / 5-bisphosphate 5-phosphatase / SH2 domain-containing inositol 5'-phosphatase 1 / SH2 domain-containing inositol phosphatase 1 / SHIP-1 / p150Ship / hp51CN


Mass: 52877.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5D, SHIP, SHIP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92835, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase, inositol-polyphosphate 5-phosphatase, phosphoinositide 5-phosphatase
#2: Chemical ChemComp-YBZ / (5-phenyl-1,3,4-thiadiazol-2-yl)methanimine


Mass: 189.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole 20 % PEG 500 MME, 10% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→62.5 Å / Num. obs: 109198 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Net I/σ(I): 11.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5345 / CC1/2: 0.581 / Rpim(I) all: 0.998 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→59.163 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.516 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1905 2038 1.868 %
Rwork0.146 107056 -
all0.147 --
obs-109094 99.983 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.198 Å20 Å2-0 Å2
2--0.299 Å20 Å2
3----0.101 Å2
Refinement stepCycle: LAST / Resolution: 1.3→59.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 25 532 4278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124090
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163836
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6575590
X-RAY DIFFRACTIONr_angle_other_deg0.6261.5748932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.8295.27818
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.32101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4110751
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.826101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.06610194
X-RAY DIFFRACTIONr_chiral_restr0.0970.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
X-RAY DIFFRACTIONr_nbd_refined0.2010.2696
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.23444
X-RAY DIFFRACTIONr_nbtor_refined0.180.21899
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2371
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2060.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.228
X-RAY DIFFRACTIONr_nbd_other0.1870.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.245
X-RAY DIFFRACTIONr_mcbond_it1.8871.8831933
X-RAY DIFFRACTIONr_mcbond_other1.8831.8821933
X-RAY DIFFRACTIONr_mcangle_it2.5683.3942435
X-RAY DIFFRACTIONr_mcangle_other2.5683.3952436
X-RAY DIFFRACTIONr_scbond_it2.1062.1712157
X-RAY DIFFRACTIONr_scbond_other2.1052.1712158
X-RAY DIFFRACTIONr_scangle_it2.9633.8453119
X-RAY DIFFRACTIONr_scangle_other2.9633.8443120
X-RAY DIFFRACTIONr_lrange_it4.13726.0794708
X-RAY DIFFRACTIONr_lrange_other3.8422.9424561
X-RAY DIFFRACTIONr_rigid_bond_restr4.6437926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.3191340.28978540.28979910.9120.92999.96250.293
1.334-1.370.2881280.27376580.27377910.9350.94199.93580.273
1.37-1.410.2741240.24674230.24775490.9450.95499.97350.243
1.41-1.4530.2281420.21272380.21373830.9680.96799.95940.205
1.453-1.5010.2331200.18469750.18570970.9610.97799.97180.17
1.501-1.5540.2111470.16767950.16869420.970.9821000.149
1.554-1.6120.1831420.14165270.14266700.980.98799.9850.12
1.612-1.6780.1751290.12963170.1364460.9820.991000.108
1.678-1.7530.2031150.12260480.12361640.9790.99199.98380.101
1.753-1.8380.1761240.11958000.1259240.9780.9911000.099
1.838-1.9370.187990.11755050.11956050.9780.99299.98220.1
1.937-2.0550.1561110.11552320.11653430.9880.9941000.105
2.055-2.1960.199950.12649170.12850120.9770.9921000.116
2.196-2.3720.171900.12446080.12546980.9850.9921000.113
2.372-2.5980.169750.11542670.11543420.9840.9921000.104
2.598-2.9040.183620.12338640.12439260.980.9911000.112
2.904-3.3520.15670.12934340.1335010.9830.991000.121
3.352-4.1020.156540.12829310.12929850.9840.991000.122
4.102-5.7870.171460.15823090.15823550.9910.9911000.153
5.787-59.1630.346340.25513540.25813890.9520.97499.9280.245

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