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- PDB-3mtc: Crystal Structure of INPP5B in complex with phosphatidylinositol ... -

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Basic information

Entry
Database: PDB / ID: 3mtc
TitleCrystal Structure of INPP5B in complex with phosphatidylinositol 4-phosphate
ComponentsType II inositol-1,4,5-trisphosphate 5-phosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / INPP5BA / Phosphoinositide 5-phosphatase / inositol signalling / phosphatase / magnesium / structural genomics / SGC / SGC Stockholm / Structural Genomics Consortium / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol ...Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol / endoplasmic reticulum-Golgi intermediate compartment / phagocytic vesicle membrane / early endosome membrane / spermatogenesis / in utero embryonic development / Golgi apparatus / signal transduction / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
INPP5B, PH domain / Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / OCRL1/INPP5B, INPP5c domain / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A ...INPP5B, PH domain / Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / OCRL1/INPP5B, INPP5c domain / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Endonuclease/exonuclease/phosphatase superfamily / Rho GTPase activation protein / 4-Layer Sandwich / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Chem-PIF / Type II inositol 1,4,5-trisphosphate 5-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2014
Title: Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases
Authors: Tresaugues, L. / Silvander, C. / Flodin, S. / Welin, M. / Nyman, T. / Graslund, S. / Hammarstrom, M. / Berglund, H. / Nordlund, P.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2087
Polymers36,2011
Non-polymers1,0076
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules

A: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules

A: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,62321
Polymers108,6033
Non-polymers3,02018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area5150 Å2
ΔGint-123 kcal/mol
Surface area39450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.761, 133.761, 133.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Type II inositol-1,4,5-trisphosphate 5-phosphatase / Phosphoinositide 5-phosphatase / 5PTase / 75 kDa inositol polyphosphate-5-phosphatase


Mass: 36201.086 Da / Num. of mol.: 1 / Fragment: UNP residues 339-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5B / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: P32019, phosphoinositide 5-phosphatase

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Non-polymers , 6 types, 231 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PIF / (2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate / L-ALPHA-D-MYOPHOSPHATIDYLINOSITOL 4-PHOSPHATE / D(+)SN1,2DI-O-OCTANOYLGLYCERYL


Mass: 666.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H48O16P2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 5.51 Å3/Da / Density % sol: 77.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% polyacrylic acid, 0.02M magnesium chloride, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009 / Details: mirrors
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.4→94.51 Å / Num. all: 31433 / Num. obs: 31380 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2 / Num. unique all: 4498 / Rsym value: 0.698 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9Y

1i9y


Resolution: 2.4→47.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.057 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20544 1580 5 %RANDOM
Rwork0.17062 ---
obs0.17234 29805 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.796 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 62 225 2797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222664
X-RAY DIFFRACTIONr_bond_other_d0.0010.021815
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9583609
X-RAY DIFFRACTIONr_angle_other_deg0.80634423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44824.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87715450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6621513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_mcbond_it0.6521.51557
X-RAY DIFFRACTIONr_mcbond_other0.0971.5631
X-RAY DIFFRACTIONr_mcangle_it1.28122520
X-RAY DIFFRACTIONr_scbond_it1.73631107
X-RAY DIFFRACTIONr_scangle_it2.8814.51086
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 119 -
Rwork0.27 2142 -
obs--98.65 %

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