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- PDB-6wrr: CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 I... -

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Basic information

Entry
Database: PDB / ID: 6wrr
TitleCRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AND LITHIUM AT 2.5 ANGSTROM RESOLUTION
ComponentsInositol polyphosphate 1-phosphatase
KeywordsSIGNALING PROTEIN / inositol phosphate / neurological disease / Bipolar disorder / manic depressive illness / phosphatase
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
GADOLINIUM ATOM / Inositol polyphosphate 1-phosphatase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsDollins, D.R. / Endo-Streeter, S. / York, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL055672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124404 United States
Howard Hughes Medical Institute (HHMI)york investigator 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
DepositionApr 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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 1.3Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)44,4845
Polymers43,9771
Non-polymers5074
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.640, 51.640, 143.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Inositol polyphosphate 1-phosphatase / IPPase


Mass: 43976.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: INPP1 / Production host: Baculoviridae sp. (virus)
References: UniProt: P21327, inositol-1,4-bisphosphate 1-phosphatase
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#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.: 85 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Description: Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions ...Description: Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions routinely exceeding 0.1 x 0.1 x 0.5mm. Gd3+, a competitive inhibitor of Mg2+, has a useful anomalous absorption edge at the CuK wavelength and therefore was used in the co-crystallization or soaking conditions.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 13% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir ...Details: 13% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir solution to 3uL hanging drops (2.5mM final Gd3+) containing native crystals for 48 hours

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Jul 10, 1992
RadiationMonochromator: supper graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→15.45 Å / Num. obs: 26197 / % possible obs: 96 % / Redundancy: 3.4 % / Rsym value: 0.051 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.69 Å / Num. unique obs: 2250 / Rsym value: 0.172 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
SQUASHphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1INP

1inp


Resolution: 2.5→15.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.952 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.616 / ESU R Free: 0.248 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20497 725 5.9 %RANDOM
Rwork0.16286 ---
obs0.16537 11645 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.228 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.56 Å2
Refinement stepCycle: 1 / Resolution: 2.5→15.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 12 85 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222569
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9693483
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22525.138109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76615439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1141511
X-RAY DIFFRACTIONr_chiral_restr0.0690.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021899
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.21044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21747
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.010.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4321.51659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74822596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.81931026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3334.5885
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 53 -
Rwork0.189 736 -
obs--99.87 %

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