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- PDB-5a7j: Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetr... -

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Basic information

Entry
Database: PDB / ID: 5a7j
TitleCrystal structure of INPP5B in complex with benzene 1,2,4,5- tetrakisphosphate
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


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-K2Y / Type II inositol 1,4,5-trisphosphate 5-phosphatase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTresaugues, L. / Mills, S.J. / Silvander, C. / Cozier, G. / Potter, B.V.L. / Nordlund, 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 2.0Oct 3, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Jan 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 / 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 / _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
B: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8039
Polymers72,4022
Non-polymers1,4007
Water1,36976
1
A: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7593
Polymers36,2011
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0436
Polymers36,2011
Non-polymers8425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.261, 94.442, 78.313
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.72408, 0.00399, -0.68971), (0.00345, -0.99999, -0.00216), (-0.68971, -0.00082, -0.72408)
Vector: 37.93526, -38.67537, 94.85277)

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Components

#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.: 2 / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K2Y / (2,4,5-triphosphonooxyphenyl) dihydrogen phosphate


Mass: 462.029 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O16P4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.61 Å3/Da / Density % sol: 52.89 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M LI2SO4, 0.1 M BIS-TRIS PH 5.5 AND 25% PEG3350

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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: Nov 1, 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: 2.9→48.48 Å / Num. obs: 16223 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 52.88 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N9V

3n9v


Resolution: 2.9→48.48 Å / Cor.coef. Fo:Fc: 0.9009 / Cor.coef. Fo:Fc free: 0.8422 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REMARK 3 NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 813 5 %RANDOM
Rwork0.1996 ---
obs0.2022 16222 99.67 %-
Displacement parametersBiso mean: 39.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.2119 Å20 Å27.4842 Å2
2---1.6898 Å20 Å2
3---6.9017 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4955 0 78 76 5109
LS refinement shellResolution: 2.9→3.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3101 144 4.93 %
Rwork0.2143 2777 -
all0.2192 2921 -
obs--99.67 %

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