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- PDB-8tfa: Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) ... -

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Basic information

Entry
Database: PDB / ID: 8tfa
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-PP-IP4, produced upon myo-(2OH)-IP5 phosphorylation by TvIPK
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / inositol phosphate / inositol / phosphatase / NUT3 / DIPP1
Function / homology
Function and homology information


inositol diphosphate pentakisphosphate diphosphatase activity / diphosphoinositol polyphosphate catabolic process / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process ...inositol diphosphate pentakisphosphate diphosphatase activity / diphosphoinositol polyphosphate catabolic process / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-polyphosphate diphosphatase / RNA decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cell-cell signaling / manganese ion binding / glutamatergic synapse / magnesium ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
FLUORIDE ION / Chem-U6J / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsZong, G. / Wang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046-31 United States
CitationJournal: Embo J. / Year: 2024
Title: Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus.
Authors: Zong, G. / Desfougeres, Y. / Portela-Torres, P. / Kwon, Y.U. / Saiardi, A. / Shears, S.B. / Wang, H.
History
DepositionJul 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9037
Polymers17,1151
Non-polymers7876
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.304, 59.640, 62.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase 1 / DIPP-1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 1 / Nucleoside diphosphate-linked ...DIPP-1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 1 / Nucleoside diphosphate-linked moiety X motif 3 / Nudix motif 3


Mass: 17115.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT3, DIPP, DIPP1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-U6J / (1r,2R,3S,4r,5R,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium ...Details: 10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium acetate, pH 5.0, 20 mM magnesium chloride, 100 mM sodium fluoride in presence of TvIPK reaction solution with 2-OH-IP5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 33485 / % possible obs: 97.2 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.4-1.427.80.64513700.9160.9780.2130.6810.41479.9
1.42-1.458.10.60414180.930.9820.1970.6380.42184.7
1.45-1.488.30.5615190.9380.9840.1820.590.44189.4
1.48-1.518.30.50215970.9540.9880.1630.5290.4794.4
1.51-1.547.90.40716450.9630.9910.1370.430.50697.5
1.54-1.588.20.38317010.9580.9890.130.4060.53198.7
1.58-1.6211.10.36816820.9850.9960.110.3850.53799.8
1.62-1.6611.90.34517040.9860.9960.1010.360.56399.9
1.66-1.7112.20.30417030.9910.9980.0890.3170.58499.9
1.71-1.7612.30.27617010.9910.9980.0810.2880.624100
1.76-1.8312.30.22917170.9920.9980.0670.2390.739100
1.83-1.912.10.20117120.9940.9980.060.210.82100
1.9-1.9911.70.16817140.9930.9980.0510.1761.01899.9
1.99-2.0910.70.13717140.9950.9990.0430.1441.21799.4
2.09-2.2210.70.11117160.9960.9990.0350.1171.34599.7
2.22-2.3913.40.09717290.99810.0280.1011.566100
2.39-2.6313.30.08917370.9970.9990.0250.0931.618100
2.63-3.0212.90.07917470.9970.9990.0230.0821.84399.8
3.02-3.811.40.0717730.9980.9990.0220.0732.34199.6
3.8-5011.50.06518860.9970.9990.020.0682.29399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→36.1 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.207 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 1668 5 %RANDOM
Rwork0.15375 ---
obs0.15453 31767 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.223 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å2-0 Å2
2---2.03 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.4→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 41 183 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181088
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.6961652
X-RAY DIFFRACTIONr_angle_other_deg1.5251.5952531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17921.11172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37815211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8731512
X-RAY DIFFRACTIONr_chiral_restr0.1520.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8092.184565
X-RAY DIFFRACTIONr_mcbond_other1.8022.177564
X-RAY DIFFRACTIONr_mcangle_it2.6843.266713
X-RAY DIFFRACTIONr_mcangle_other2.6863.273714
X-RAY DIFFRACTIONr_scbond_it3.6912.675642
X-RAY DIFFRACTIONr_scbond_other3.7092.685634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7013.867924
X-RAY DIFFRACTIONr_long_range_B_refined7.0428.5131404
X-RAY DIFFRACTIONr_long_range_B_other6.86727.5771353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.432 Å
RfactorNum. reflection% reflection
Rfree0.239 85 -
Rwork0.254 1868 -
obs--77.65 %

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