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- PDB-5a7i: Crystal structure of INPP5B in complex with biphenyl 3,3',4,4',5,... -

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Basic information

Entry
Database: PDB / ID: 5a7i
TitleCrystal structure of INPP5B in complex with biphenyl 3,3',4,4',5,5'- hexakisphosphate
ComponentsTYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE
KeywordsHYDROLASE / SGC / SIGNALLING / STRUCTURAL GENOMICS CONSORTIUM STOCKHOLM / MAGNESIUM BINDING / PROTEIN-INHBITOR COMPLEX / INHIBITOR / PHOSPHOINOSITIDES SIGNALLING
Function / homology
Function and homology information


inositol-1,4,5-trisphosphate 5-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / flagellated sperm motility / regulation of protein processing / endoplasmic reticulum-Golgi intermediate compartment ...inositol-1,4,5-trisphosphate 5-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / flagellated sperm motility / regulation of protein processing / endoplasmic reticulum-Golgi intermediate compartment / Synthesis of IP3 and IP4 in the cytosol / phagocytic vesicle membrane / early endosome membrane / spermatogenesis / in utero embryonic development / neuron projection / Golgi apparatus / signal transduction / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
INPP5B, PH domain / Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain / OCRL1/INPP5B, INPP5c domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / : / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues ...INPP5B, PH domain / Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain / OCRL1/INPP5B, INPP5c domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / : / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / 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 / Rho GTPase activation protein / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biphenyl 3,3',4,4',5,5'-hexakisphosphate / PHOSPHATE ION / Type II inositol 1,4,5-trisphosphate 5-phosphatase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsTresaugues, L. / Mills, S.J. / Silvander, C. / Cozier, G. / Potter, B.V.L. / Norldund, P.
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase Inpp5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family.
Authors: Mills, S.J. / Silvander, C. / Cozier, G. / Tresaugues, L. / Nordlund, P. / Potter, B.V.L.
History
DepositionJul 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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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)37,3688
Polymers36,2011
Non-polymers1,1677
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.975, 96.975, 152.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 / 75 KDA INOSITOL POLYPHOSPHATE-5-PHOSPHATASE / PHOSPHOINOSITIDE 5-PHOSPHATASE / 5PTASE / TYPE II ...75 KDA INOSITOL POLYPHOSPHATE-5-PHOSPHATASE / PHOSPHOINOSITIDE 5-PHOSPHATASE / 5PTASE / TYPE II INOSITOL 1 / 4 / 5-TRISPHOSPHATE 5-PHOSPHATASE / ISOFORM 2


Mass: 36201.086 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 339-643
Source method: isolated from a genetically manipulated source
Details: CLONED WITH A C-TERMINAL HEXAHISTIDINE TAG / Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: P32019, phosphoinositide 5-phosphatase

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Non-polymers , 6 types, 35 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-B6K / Biphenyl 3,3',4,4',5,5'-hexakisphosphate


Mass: 730.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16O24P6
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.96 Å3/Da / Density % sol: 75.2 % / Description: NONE
Crystal growpH: 6.2
Details: 10% GLYCEROL, 25% PROPANEDIOL AND 0.1 M SODIUM/POTASSIUM PHOSPHATE PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.89→34.29 Å / Num. obs: 16922 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.2
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N9V

3n9v


Resolution: 2.89→34.29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 22.814 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22324 858 5.1 %RANDOM
Rwork0.197 ---
obs0.19826 16012 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.185 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---1.25 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.89→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 65 28 2638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212682
X-RAY DIFFRACTIONr_bond_other_d0.0020.021782
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.963645
X-RAY DIFFRACTIONr_angle_other_deg0.77134329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7624.135133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13715448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1771513
X-RAY DIFFRACTIONr_chiral_restr0.0640.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2371.51561
X-RAY DIFFRACTIONr_mcbond_other0.031.5633
X-RAY DIFFRACTIONr_mcangle_it0.45622524
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.64131121
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1324.51120
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 66 -
Rwork0.338 1148 -
obs--100 %
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)
13.3791-0.6452-1.01425.29611.78292.33610.01670.3588-0.3907-0.65520.10740.30.292-0.2728-0.1240.3405-0.1389-0.1091-0.00740.07920.173817.5772-30.186420.5714
27.9608-3.1494-1.86313.07520.83613.7962-0.1712-0.40440.47490.08930.4635-0.9548-0.15720.4095-0.29230.2697-0.16250.129-0.0189-0.01190.202126.8076-16.71922.7778
31.6466-0.6384-0.37645.71350.23121.68710.17170.93170.3607-1.49530.17270.1132-0.498-0.3559-0.34440.8245-0.1131-0.08370.39370.20060.180117.2144-18.18827.5988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A258 - 399
2X-RAY DIFFRACTION2A400 - 448
3X-RAY DIFFRACTION3A449 - 570

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