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- PDB-7kir: Crystal structure of inositol polyphosphate 1-phosphatase (INPP1)... -

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Basic information

Entry
Database: PDB / ID: 7kir
TitleCrystal structure of inositol polyphosphate 1-phosphatase (INPP1) D54A mutant in complex with inositol (1,4)-bisphosphate
ComponentsInositol polyphosphate 1-phosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


inositol-1,3,4-trisphosphate 1-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / metal ion binding
Similarity search - Function
Inositol polyphosphate 1-phosphatase, domain 1 / : / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4-BISPHOSPHATE / Inositol polyphosphate 1-phosphatase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDollins, D.E. / Xiong, J.-P. / Ren, Y. / York, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM124404 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL055672 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A structural basis for lithium and substrate binding of an inositide phosphatase.
Authors: Dollins, D.E. / Xiong, J.P. / Endo-Streeter, S. / Anderson, D.E. / Bansal, V.S. / Ponder, J.W. / Ren, Y. / York, J.D.
History
DepositionOct 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol polyphosphate 1-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3534
Polymers43,9331
Non-polymers4203
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.437, 51.437, 142.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Inositol polyphosphate 1-phosphatase / IPPase


Mass: 43932.922 Da / Num. of mol.: 1 / Mutation: D54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: INPP1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21327, inositol-1,4-bisphosphate 1-phosphatase
#2: Chemical ChemComp-2IP / D-MYO-INOSITOL-1,4-BISPHOSPHATE


Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Crystals were first grown in 0.1M sodium citrate pH 4.3, 16-18% PEG6K, 5 mM CaCl2. Then crystals were soaked with inositol (1,4)-bisphosphate for 1-3 hours

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→35.3 Å / Num. obs: 10601 / % possible obs: 92.8 % / Biso Wilson estimate: 31.65 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.8
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 929

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1INP

1inp


Resolution: 2.6→35.25 Å / SU ML: 0.321 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.9723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 1070 10.1 %
Rwork0.1904 9525 -
obs0.196 10595 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.83 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 22 22 2585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472604
X-RAY DIFFRACTIONf_angle_d0.76093526
X-RAY DIFFRACTIONf_chiral_restr0.0484409
X-RAY DIFFRACTIONf_plane_restr0.0037445
X-RAY DIFFRACTIONf_dihedral_angle_d11.4329344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.32741200.27831061X-RAY DIFFRACTION82.36
2.72-2.860.29031340.25681174X-RAY DIFFRACTION91.66
2.86-3.040.32061360.22261231X-RAY DIFFRACTION95.46
3.04-3.280.27581400.18951227X-RAY DIFFRACTION97.43
3.28-3.610.21291360.18121223X-RAY DIFFRACTION96.18
3.61-4.130.25261370.16341232X-RAY DIFFRACTION96.41
4.13-5.20.18131420.15451220X-RAY DIFFRACTION94.45
5.2-35.250.23651250.19141157X-RAY DIFFRACTION89.28

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