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

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Basic information

Entry
Database: PDB / ID: 7kio
TitleCrystal structure of inositol polyphosphate 1-phosphatase (INPP1) D54A mutant
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
Inositol polyphosphate 1-phosphatase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXiong, J.-P. / Dollins, D.E. / 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)44,1654
Polymers43,9331
Non-polymers2323
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.447, 51.447, 143.118
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Citrate pH 4.3, 16-18% PEG6000, 5 mM CaCl2

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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: 2.4→28.93 Å / Num. obs: 14352 / % possible obs: 98.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.401 / Num. unique obs: 1311

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Processing

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

1inp


Resolution: 2.4→28.93 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.7232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 862 6.01 %
Rwork0.1906 13490 -
obs0.1936 14352 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 11 47 2592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482585
X-RAY DIFFRACTIONf_angle_d0.75033496
X-RAY DIFFRACTIONf_chiral_restr0.0501401
X-RAY DIFFRACTIONf_plane_restr0.004444
X-RAY DIFFRACTIONf_dihedral_angle_d14.8857341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.26261320.21522098X-RAY DIFFRACTION91.73
2.55-2.740.28381530.21282256X-RAY DIFFRACTION99.71
2.74-3.020.2761410.21342292X-RAY DIFFRACTION99.84
3.02-3.450.26541480.19072285X-RAY DIFFRACTION99.92
3.46-4.350.22081320.17572280X-RAY DIFFRACTION99.55
4.35-28.930.21091560.18152279X-RAY DIFFRACTION99.23

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