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- PDB-5rxm: INPP5D PanDDA analysis group deposition -- Crystal Structure of t... -

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Basic information

Entry
Database: PDB / ID: 5rxm
TitleINPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434894
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / SHIP1 / Alzheimers
Function / homology
Function and homology information


inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-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 ...inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-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 / negative regulation of immune response / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / 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 / PECAM1 interactions / Synthesis of PIPs at the plasma membrane / negative regulation of interleukin-6 production / regulation of immune response / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / 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
Similarity search - Function
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
Chem-GWV / Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.46 Å
AuthorsBradshaw, W.J. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O.
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
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: 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 / database_2
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 / _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
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3826
Polymers52,8781
Non-polymers5055
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint12 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 78.990, 89.080
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 / 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 / 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-GWV / ~{N},~{N}-dimethyl-4-[(propan-2-ylamino)methyl]aniline


Mass: 192.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.07 Å3/Da / Density % sol: 40.69 % / Mosaicity: 0 °
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 sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.46→59.1 Å / Num. obs: 77044 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.046 / Rrim(I) all: 0.116 / Net I/σ(I): 9.6 / Num. measured all: 486855 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.46-1.55.21.5492933156030.4380.751.7251
6.53-59.160.03860319970.9980.0170.04132.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 6XY7

6xy7


Resolution: 1.46→59.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.834 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 3841 5 %RANDOM
Rwork0.1705 ---
obs0.1719 73130 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.51 Å2 / Biso mean: 18.746 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.92 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.46→59.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 30 439 4169
Biso mean--21.31 29.68 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0157841
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185027
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6577836
X-RAY DIFFRACTIONr_angle_other_deg1.4281.611892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1722.701311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.672151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1451538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027158
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021292
X-RAY DIFFRACTIONr_mcbond_it1.421.7543763
X-RAY DIFFRACTIONr_mcbond_other1.4181.7453731
X-RAY DIFFRACTIONr_mcangle_it2.6012.653717
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 300 -
Rwork0.299 5292 -
all-5592 -
obs--99.93 %

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