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- PDB-8t99: Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) ... -

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Basic information

Entry
Database: PDB / ID: 8t99
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-L-1,4-[PP]2-(2,3)IP2, Mg, and Fluoride ion
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / inositol phosphate / inositol / phosphatase / NUT3
Function / homology
Function and homology information


diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity ...diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process / RNA decapping / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / Synthesis of pyrophosphates in the cytosol / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cell-cell signaling / manganese ion binding / magnesium ion binding / zinc ion binding / nucleus / cytosol / cytoplasm
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-ZOW / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 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
DepositionJun 23, 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)17,9388
Polymers17,1151
Non-polymers8237
Water3,729207
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)45.824, 59.634, 62.653
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, 214 molecules

#2: Chemical ChemComp-ZOW / (1R,2S,3S,4R,5S,6S)-2,3-dihydroxy-5,6-bis(phosphonooxy)cyclohexane-1,4-diyl bis[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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-F / FLUORIDE ION / Fluoride


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 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 L-scyllo-(1,2,3,4)IP4

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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: 1.5→50 Å / Num. obs: 26499 / % possible obs: 94.2 % / Redundancy: 10 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.538.30.48810660.9280.9810.1680.5180.4477.2
1.53-1.558.10.41710380.9330.9830.1450.4430.46475.7
1.55-1.588.50.41612180.950.9870.1420.4420.46487.8
1.58-1.629.50.3913140.9590.990.1280.4120.46895.6
1.62-1.659.90.35813300.9750.9940.1160.3780.596.7
1.65-1.6910.30.32913610.9760.9940.1060.3460.50597.2
1.69-1.7310.30.30813510.980.9950.10.3240.50597.5
1.73-1.7810.40.2613540.9870.9970.0840.2740.54997.6
1.78-1.8310.40.22713500.9890.9970.0740.2390.58597.6
1.83-1.8910.20.20413660.9880.9970.0670.2150.60698.1
1.89-1.969.90.16513710.9890.9970.0550.1740.70898.3
1.96-2.049.50.14413670.9910.9980.0490.1520.76998.3
2.04-2.138.90.12212430.9930.9980.0420.130.86988.2
2.13-2.2410.40.10413010.9950.9990.0330.1090.93893.4
2.24-2.3811.30.09113970.9970.9990.0280.0961.02498.9
2.38-2.5611.20.07914080.9970.9990.0240.0831.06499.2
2.56-2.82110.07314020.9970.9990.0230.0761.18699.2
2.82-3.2310.50.06514270.9980.9990.0210.0681.48199.3
3.23-4.079.50.05513260.9980.9990.0180.0581.79990.7
4.07-5010.50.04815090.99910.0150.051.50597.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→31.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.362 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18271 1318 5 %RANDOM
Rwork0.156 ---
obs0.15732 25145 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.491 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å2-0 Å2
2---1.53 Å20 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.5→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 42 207 1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181115
X-RAY DIFFRACTIONr_angle_refined_deg2.011.6881706
X-RAY DIFFRACTIONr_angle_other_deg1.4991.5932599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98621.33375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4315218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1171512
X-RAY DIFFRACTIONr_chiral_restr0.2040.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021397
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02275
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_it1.5721.586579
X-RAY DIFFRACTIONr_mcbond_other1.5731.58578
X-RAY DIFFRACTIONr_mcangle_it2.3822.367734
X-RAY DIFFRACTIONr_mcangle_other2.3822.374735
X-RAY DIFFRACTIONr_scbond_it3.0832.028663
X-RAY DIFFRACTIONr_scbond_other3.0622.011655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.782.873955
X-RAY DIFFRACTIONr_long_range_B_refined7.18321.6241462
X-RAY DIFFRACTIONr_long_range_B_other7.00720.4021396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 63 -
Rwork0.231 1459 -
obs--74.57 %

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