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- PDB-2xsw: Crystal structure of human INPP5E -

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Basic information

Entry
Database: PDB / ID: 2xsw
TitleCrystal structure of human INPP5E
Components72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE
KeywordsHYDROLASE / INOSITOL SIGNALLING / SGC STOCKHOLM / STRUCTURAL GENOMICS CONSORTIUM
Function / homology
Function and homology information


negative regulation of protein localization to cilium / : / : / ARL13B-mediated ciliary trafficking of INPP5E / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ...negative regulation of protein localization to cilium / : / : / ARL13B-mediated ciliary trafficking of INPP5E / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / phosphatidylinositol biosynthetic process / Golgi cisterna membrane / axoneme / ruffle / cilium / negative regulation of translation / plasma membrane / cytosol
Similarity search - Function
72kDa inositol polyphosphate 5-phosphatase / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol polyphosphate 5-phosphatase type IV
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTresaugues, L. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Schutz, P. / 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. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Nordlund, P.
CitationJournal: To be Published
Title: Crystal Structure of Human Inpp5E
Authors: Tresaugues, L. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Tresaugues, L. / Schutz, P. / 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. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Siponen, M.I. / Thorsell, A.G. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Nordlund, P.
History
DepositionSep 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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

Downloads & links

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Assembly

Deposited unit
A: 72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE
B: 72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,40910
Polymers80,9562
Non-polymers4548
Water6,395355
1
A: 72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7686
Polymers40,4781
Non-polymers2915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6414
Polymers40,4781
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.528, 103.579, 137.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE / PHOSPHATIDYLINOSITOL-4\ / 5-BISPHOSPHATE 5-PHOSPHATASE / PHOSPHATIDYLINOSITOL POLYPHOSPHATE 5- ...PHOSPHATIDYLINOSITOL-4\ / 5-BISPHOSPHATE 5-PHOSPHATASE / PHOSPHATIDYLINOSITOL POLYPHOSPHATE 5-PHOSPHATASE TYPE IV


Mass: 40477.949 Da / Num. of mol.: 2 / Fragment: PHOSPHATASE DOMAIN, RESIDUES 275-623
Source method: isolated from a genetically manipulated source
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)R3 PRARE / References: UniProt: Q9NRR6, phosphoinositide 5-phosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.23 Å3/Da / Density % sol: 44.78 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS INCUBATE WITH 1MM PHOSPHATIDYLINOSITOL-3,4,5-TRIPHOSPHATE AND 2MM MGCL2 PRIOR SETTING-UP THE PLATES. PROTEIN WAS THEN CRYSTALLIZED AGAINST 0.2M MGCL2, 10% W/V PEG8K AND 0.1M TRIS PH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0714
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0714 Å / Relative weight: 1
ReflectionResolution: 1.9→48.47 Å / Num. obs: 56918 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 26.75 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9Y
Resolution: 1.9→48.468 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1947 2895 5.1 %
Rwork0.1649 --
obs0.1665 56829 98.33 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.381 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.4205 Å20 Å2-0 Å2
2--3.8315 Å20 Å2
3----2.411 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5338 0 23 355 5716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115579
X-RAY DIFFRACTIONf_angle_d1.2877578
X-RAY DIFFRACTIONf_dihedral_angle_d12.8932067
X-RAY DIFFRACTIONf_chiral_restr0.094832
X-RAY DIFFRACTIONf_plane_restr0.005978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.2942910.23295248X-RAY DIFFRACTION97
1.9679-2.04670.2172790.17545252X-RAY DIFFRACTION97
2.0467-2.13990.21352970.15575278X-RAY DIFFRACTION98
2.1399-2.25270.20322650.15335376X-RAY DIFFRACTION98
2.2527-2.39380.21832760.16475339X-RAY DIFFRACTION98
2.3938-2.57860.22022940.16995346X-RAY DIFFRACTION99
2.5786-2.83810.20712950.17035374X-RAY DIFFRACTION98
2.8381-3.24870.20962800.16965470X-RAY DIFFRACTION99
3.2487-4.09270.18142920.15775521X-RAY DIFFRACTION99
4.0927-48.48340.1623260.15925730X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2475-0.14780.24851.5959-0.74111.4843-0.02950.0112-0.1276-0.00220.05610.14640.0946-0.1924-0.01540.1421-0.02550.01940.1369-0.01490.1365-8.9123-27.897238.3173
21.2990.0239-0.03591.9756-0.68571.6949-0.06860.17880.132-0.19090.0878-0.0077-0.0734-0.0247-0.00490.0748-0.03120.01380.08920.00650.08570.0695-17.268526.1934
31.52010.05340.02231.4857-0.7552.1976-0.06290.0784-0.0748-0.03690.03870.02510.0563-0.10610.02080.1008-0.0284-0.00510.0762-0.04210.1155-5.4267-26.896533.581
41.4892-0.18510.43121.0909-0.07992.6004-0.0276-0.04730.00430.01620.0278-0.0598-0.04780.23580.00910.1587-0.0185-0.03090.1813-0.00260.118222.4389-8.691170.9744
51.6357-0.06230.40881.50240.15042.8163-0.090.21990.1646-0.25630.02050.0777-0.3728-0.1640.05050.1699-0.0027-0.06160.11650.0310.106813.7701-1.538955.5505
61.1122-0.25520.69311.5686-0.24552.4382-0.0977-0.01630.0889-0.0160.068-0.0526-0.20930.0260.03130.1331-0.0204-0.02480.1625-0.02320.132219.8858-4.43168.9848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 282:382)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 383:547)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 548:624)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 282:393)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 394:544)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 551:623)

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