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- PDB-4cml: Crystal Structure of INPP5B in complex with Phosphatidylinositol ... -

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Basic information

Entry
Database: PDB / ID: 4cml
TitleCrystal Structure of INPP5B in complex with Phosphatidylinositol 3,4- bisphosphate
ComponentsTYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2
KeywordsHYDROLASE / SGC / SIGNALLING / STRUCTURAL GENOMICS CONSORTIUM STOCKHOLM / MAGNESIUM BINDING
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-52N / Type II inositol 1,4,5-trisphosphate 5-phosphatase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Moche, M. ...Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Moche, M. / Nyman, T. / Schuler, H. / Silvander, C. / Thorsell, A.G. / Weigelt, J. / Welin, M. / Nordlund, P.
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
DepositionJan 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: 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.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.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_conn.ptnr2_label_seq_id / _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, ISOFORM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1966
Polymers36,2011
Non-polymers9945
Water5,765320
1
A: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2
hetero molecules

A: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2
hetero molecules

A: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,58718
Polymers108,6033
Non-polymers2,98315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
Buried area4170 Å2
ΔGint-118.7 kcal/mol
Surface area39380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.661, 133.661, 133.661
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, ISOFORM 2 / 75 KDA INOSITOL POLYPHOSPHATE-5-PHOSPHATASE / PHOSPHOINOSITIDE 5-PHOSPHATASE / 5PTASE


Mass: 36201.086 Da / Num. of mol.: 1 / Fragment: 5-PHOSPHATASE CATALYTIC DOMAIN, RESIDUES 259-563
Source method: isolated from a genetically manipulated source
Details: DOMAIN ENCOMPASSING RESIDUES 259 TO 563. CLONED WITH A C-TERMINAL HEXAHISTIDINE TAG.
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION / 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, 325 molecules

#2: Chemical ChemComp-52N / 1,2-dioctanoyl phosphatidyl epi-inositol (3,4)-bisphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA HEXAHISTIDINE TAG AND AN EXTRA ALANINE WERE ADDED IN C- TERMINUS.

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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: 5.58 Å3/Da / Density % sol: 77.98 % / Description: NONE
Crystal growpH: 7
Details: 1.1 M NA-MALONATE PH 7.0, 0.1 M HEPES PH 7.0, 0.5% JEFFAMINE ED-2001 PH 7.0, 2MM MGSO4, 2MM PTDINS-(3,4,5)-P3 (1,2-DIOCTANOYL)

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2010 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2.3→29.89 Å / Num. obs: 35595 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N9V

3n9v


Resolution: 2.3→28.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.189 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 1786 5 %RANDOM
Rwork0.17506 ---
obs0.17628 33778 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.567 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 60 320 2876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222633
X-RAY DIFFRACTIONr_bond_other_d0.0010.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9563573
X-RAY DIFFRACTIONr_angle_other_deg0.7834298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82424.341129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00115431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6791512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
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_it0.4361.51551
X-RAY DIFFRACTIONr_mcbond_other0.091.5629
X-RAY DIFFRACTIONr_mcangle_it0.86122507
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42231082
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3514.51065
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 113 -
Rwork0.329 2473 -
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)
14.20390.61050.171.00710.15581.10950.04920.06670.05070.0294-0.05960.0127-0.108-0.00430.01040.0828-0.00250.02290.0109-0.01210.03976.233927.9053-46.2963
24.2792-0.502-0.29172.0124-0.22341.7491-0.0558-0.1781-0.4480.16370.0146-0.11480.11430.08440.04120.077-0.02070.01360.0271-0.0010.10537.485914.915-43.1725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A258 - 421
2X-RAY DIFFRACTION2A422 - 567

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