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- PDB-1i9z: CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 5-PHOSPHATASE DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1i9z
TitleCRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 5-PHOSPHATASE DOMAIN (IPP5C) OF SPSYNAPTOJANIN IN COMPLEX WITH INOSITOL (1,4)-BISPHOSPHATE AND CALCIUM ION
ComponentsPHOSPHATIDYLINOSITOL PHOSPHATE PHOSPHATASE
KeywordsHYDROLASE / SpSynaptojanin / IPP5C / IP3 / IP2
Function / homology
Function and homology information


inositol-2,4,5-triphosphate 5-phosphatase activity / inositol-4,5,6-triphosphate 5-phosphatase activity / inositol-1,2,4,5-tetrakisphosphate 5-phosphatase activity / inositol-2,4,5,6-tetrakisphosphate 5-phosphatase activity / inositol-1,2,4,5,6-pentakisphosphate 5-phosphatase activity / Synthesis of PIPs at the plasma membrane / Synthesis of IP2, IP, and Ins in the cytosol / Synthesis of IP3 and IP4 in the cytosol / inositol-4,5-bisphosphate 5-phosphatase activity / Clathrin-mediated endocytosis ...inositol-2,4,5-triphosphate 5-phosphatase activity / inositol-4,5,6-triphosphate 5-phosphatase activity / inositol-1,2,4,5-tetrakisphosphate 5-phosphatase activity / inositol-2,4,5,6-tetrakisphosphate 5-phosphatase activity / inositol-1,2,4,5,6-pentakisphosphate 5-phosphatase activity / Synthesis of PIPs at the plasma membrane / Synthesis of IP2, IP, and Ins in the cytosol / Synthesis of IP3 and IP4 in the cytosol / inositol-4,5-bisphosphate 5-phosphatase activity / Clathrin-mediated endocytosis / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / cell tip / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / phosphatidylinositol dephosphorylation / cell division site / protein transport / calcium ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / 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 superfamily ...SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / 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 superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4-BISPHOSPHATE / Inositol-1,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.8 Å
AuthorsTsujishita, Y. / Guo, S. / Stolz, L. / York, J.D. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Specificity determinants in phosphoinositide dephosphorylation: crystal structure of an archetypal inositol polyphosphate 5-phosphatase.
Authors: Tsujishita, Y. / Guo, S. / Stolz, L.E. / York, J.D. / Hurley, J.H.
History
DepositionMar 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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: PHOSPHATIDYLINOSITOL PHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4743
Polymers40,0941
Non-polymers3802
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.999, 67.705, 51.995
Angle α, β, γ (deg.)90.0, 106.152, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHOSPHATIDYLINOSITOL PHOSPHATE PHOSPHATASE / SYNAPTOJANIN


Mass: 40094.215 Da / Num. of mol.: 1 / Fragment: IPP5C DOMAIN, RESIDUES 534-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O43001
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2IP / D-MYO-INOSITOL-1,4-BISPHOSPHATE


Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 8
Details: sodium chloride, tris, 2-mercaptoethanol, pH 8.0, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein11
2150 mM12NaCl
320 mMTris-HCl12
410 mMMPD12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32 Å / % possible obs: 95.6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.8
Reflection shellHighest resolution: 1.8 Å / Rsym value: 14.5 / % possible all: 82.4
Reflection
*PLUS
Num. obs: 44082 / Num. measured all: 148755
Reflection shell
*PLUS
% possible obs: 82.4 % / Rmerge(I) obs: 0.145

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→32 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.218 -RANDOM
Rwork0.191 --
obs-43044 -
Refinement stepCycle: LAST / Resolution: 1.8→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 21 224 3011
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 32 Å / % reflection Rfree: 10 % / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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