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- PDB-8pdg: The phosphatase and C2 domains of SHIP1 with covalent Z2738285202 -

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Basic information

Entry
Database: PDB / ID: 8pdg
TitleThe phosphatase and C2 domains of SHIP1 with covalent Z2738285202
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / ligand / phosphatase / 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 / cytoplasm / cytosol
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
~{N}-(8-chloranylquinolin-2-yl)propanamide / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBradshaw, W.J. / Moreira, T. / Scacioc, A. / 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 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3475
Polymers52,8781
Non-polymers4694
Water9,494527
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.674, 79.378, 89.573
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 of 145 kDa / SIP-145 / SH2 domain-containing inositol 5'- ...Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 / SH2 domain-containing inositol 5'-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 / Plasmid: pFB-HGT-LIC / 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-YBP / ~{N}-(8-chloranylquinolin-2-yl)propanamide


Mass: 234.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN2O / 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.: 527 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
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: 1.4→79.4 Å / Num. obs: 88594 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 8.5
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 4478 / CC1/2: 0.444

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→49.238 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.789 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.19 2160 2.441 %
Rwork0.1371 86325 -
all0.138 --
obs-88485 99.969 %
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: 19.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.534 Å20 Å2-0 Å2
2--0.979 Å20 Å2
3----0.445 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 28 527 4276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134021
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173764
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.6455483
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5768745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.235513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59523.462208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45815727
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg11.216151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3511517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02924
X-RAY DIFFRACTIONr_nbd_refined0.2250.2706
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23494
X-RAY DIFFRACTIONr_nbtor_refined0.170.21876
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21959
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2378
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.228
X-RAY DIFFRACTIONr_nbd_other0.1780.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_mcbond_it3.1411.7041901
X-RAY DIFFRACTIONr_mcbond_other3.1431.7031900
X-RAY DIFFRACTIONr_mcangle_it3.9822.5642388
X-RAY DIFFRACTIONr_mcangle_other3.9812.5662389
X-RAY DIFFRACTIONr_scbond_it8.2032.0952120
X-RAY DIFFRACTIONr_scbond_other8.2012.0942121
X-RAY DIFFRACTIONr_scangle_it8.0122.9543068
X-RAY DIFFRACTIONr_scangle_other8.0112.9543069
X-RAY DIFFRACTIONr_lrange_it7.48621.7474616
X-RAY DIFFRACTIONr_lrange_other7.44821.0734487
X-RAY DIFFRACTIONr_rigid_bond_restr3.86137785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2621470.2596286X-RAY DIFFRACTION99.9689
1.436-1.4760.2641610.2336144X-RAY DIFFRACTION99.9208
1.476-1.5180.2711500.2176006X-RAY DIFFRACTION99.9026
1.518-1.5650.2781170.1925815X-RAY DIFFRACTION99.9326
1.565-1.6160.2271280.1645671X-RAY DIFFRACTION99.9655
1.616-1.6730.2151320.1545452X-RAY DIFFRACTION99.9642
1.673-1.7360.2291350.1355309X-RAY DIFFRACTION100
1.736-1.8070.1611350.1175070X-RAY DIFFRACTION99.9808
1.807-1.8870.1791380.1134860X-RAY DIFFRACTION99.96
1.887-1.9790.161230.1024668X-RAY DIFFRACTION100
1.979-2.0860.1541090.1044482X-RAY DIFFRACTION100
2.086-2.2130.161200.0994193X-RAY DIFFRACTION100
2.213-2.3650.188960.1023986X-RAY DIFFRACTION100
2.365-2.5540.1691060.1043699X-RAY DIFFRACTION100
2.554-2.7980.153870.1173448X-RAY DIFFRACTION99.9717
2.798-3.1270.204760.1343115X-RAY DIFFRACTION100
3.127-3.6090.158700.1412774X-RAY DIFFRACTION100
3.609-4.4160.192530.1282377X-RAY DIFFRACTION100
4.416-6.2280.196410.1481869X-RAY DIFFRACTION100
6.228-49.2380.223360.2091101X-RAY DIFFRACTION99.8244

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