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- PDB-6dlg: Crystal structure of a SHIP1 surface entropy reduction mutant -

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Basic information

Entry
Database: PDB / ID: 6dlg
TitleCrystal structure of a SHIP1 surface entropy reduction mutant
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / PI3K / PIP3 / PI-3 / 4-P2 / apoptosis / immunity
Function / homology
Function and homology information


inositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol trisphosphate phosphatase activity / PECAM1 interactions / Synthesis of IP3 and IP4 in the cytosol / negative regulation of B cell activation / negative regulation of granulocyte differentiation / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation ...inositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol trisphosphate phosphatase activity / PECAM1 interactions / Synthesis of IP3 and IP4 in the cytosol / negative regulation of B cell activation / negative regulation of granulocyte differentiation / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / positive regulation of lymphocyte differentiation / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / Downstream TCR signaling / 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 / negative regulation of immune response / negative regulation of bone resorption / PTB domain binding / positive regulation of B cell differentiation / cortical cytoskeleton / negative regulation of B cell proliferation / negative regulation of osteoclast differentiation / negative regulation of interleukin-6 production / immunoglobulin mediated immune response / negative regulation of signal transduction / positive regulation of erythrocyte differentiation / determination of adult lifespan / actin filament / SH3 domain binding / intracellular signal transduction / positive regulation of apoptotic process / membrane raft / negative regulation of cell population proliferation / apoptotic process / plasma membrane / cytosol
Similarity search - Function
Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase 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
ISOPROPYL ALCOHOL / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsGardill, B.R. / Cheung, S.T. / Mui, A.L. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-84539 Canada
CitationJournal: Biorxiv / Year: 2020
Title: Interleukin-10 and Small Molecule SHIP1 Allosteric Regulators Trigger Anti-Inflammatory Effects Through SHIP1/STAT3 Complexes
Authors: Chamberlain, T.C. / Cheung, S.T. / Yoon, J.S.J. / Ming-Lum, A. / Gardill, B.R. / Shakibakho, S. / Dzananovic, E. / Ban, F. / Samiea, A. / Jawanda, K. / Priatel, J. / Krystal, G. / Ong, C.J. ...Authors: Chamberlain, T.C. / Cheung, S.T. / Yoon, J.S.J. / Ming-Lum, A. / Gardill, B.R. / Shakibakho, S. / Dzananovic, E. / Ban, F. / Samiea, A. / Jawanda, K. / Priatel, J. / Krystal, G. / Ong, C.J. / Cherkasov, A. / Andersen, R.J. / McKenna, S.A. / Van Petegem, F. / Mui, A.L.
History
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5672
Polymers52,5071
Non-polymers601
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.098, 73.200, 124.207
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


Mass: 52507.281 Da / Num. of mol.: 1 / Mutation: E770A, E772A, E773A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Inpp5d, 7a33, Ship, Ship1 / Plasmid: pET28 / Details (production host): LIC-HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): (DE3) placI
References: UniProt: Q9ES52, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1M HEPES-NaOH pH6.7, 20% PEG 1500, 5mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2015
RadiationMonochromator: Double crystal cryo cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. obs: 66070 / % possible obs: 98.9 % / Redundancy: 3.28 % / Biso Wilson estimate: 25.381 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 13.79
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.29 % / Mean I/σ(I) obs: 1.85 / Num. unique obs: 10528 / CC1/2: 0.682 / Rrim(I) all: 0.787 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→38.396 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.49
RfactorNum. reflection% reflection
Rfree0.2004 1960 2.97 %
Rwork0.1785 --
obs0.1792 66062 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.51 Å2 / Biso mean: 24.7157 Å2 / Biso min: 10.06 Å2
Refinement stepCycle: final / Resolution: 1.499→38.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 4 246 3613
Biso mean--26.56 30.87 -
Num. residues----420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4994-1.53690.30471200.27074476459698
1.5369-1.57840.29031220.23714531465399
1.5784-1.62490.24361410.22984551469299
1.6249-1.67730.23511360.21984529466599
1.6773-1.73730.24861600.19874539469999
1.7373-1.80680.23111510.18245384689100
1.8068-1.8890.21520.16745574709100
1.889-1.98860.18811410.174554469599
1.9886-2.11320.19521410.17174568470999
2.1132-2.27640.19091390.16984595473499
2.2764-2.50540.19271310.17574611474299
2.5054-2.86780.20731370.18554643478099
2.8678-3.61280.17661510.1754640479198
3.6128-38.40850.19081380.16244770490897
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)
10.86550.01470.05840.70110.06860.47110.0082-0.022-0.01170.0006-0.0058-0.0080.02260.01250.00010.12620.0039-0.00010.1042-0.00680.1203-13.6071.17-3.239
20.1019-0.2046-0.01930.3754-0.03170.49910.03910.24670.1069-0.1988-0.1007-0.12370.0438-0.0937-0.22490.19370.01170.00460.30660.08790.1784-15.32214.721-34.139
30.01340.0206-0.02810.0840.01730.13390.04370.02320.1186-0.0189-0.04290.044-0.1677-0.0095-0.01270.1860.02740.00140.24380.07260.2114-15.60417.049-26.123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A399 - 734
2X-RAY DIFFRACTION2A735 - 816
3X-RAY DIFFRACTION3A817 - 855

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