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- PDB-7tn4: Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) ... -

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Basic information

Entry
Database: PDB / ID: 7tn4
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 3-diphosphoinositol 1,2,4,5-tetrakisphosphate (3-PP-IP4), Mg and Fluoride ion
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / Phosphatase / inositol pyrophosphate / signal transduction / NUDT3
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-ZM2 / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Faseb J. / Year: 2022
Title: Structural and catalytic analyses of the InsP 6 kinase activities of higher plant ITPKs.
Authors: Zong, G. / Shears, S.B. / Wang, H.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)20,3208
Polymers19,4971
Non-polymers8237
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-51 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.149, 59.743, 62.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 19496.975 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, 141 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: 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
#5: Chemical ChemComp-ZM2 / (1R,2S,3R,4R,5S,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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
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 ZmITPK1 reaction solution with 1,2,3,4,5-IP5
PH range: 4-5

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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: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 14853 / % possible obs: 99.5 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.036 / Rrim(I) all: 0.122 / Χ2: 0.92 / Net I/σ(I): 8.4 / Num. measured all: 165071
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.889.90.387260.9820.1220.3990.87298.4
1.88-1.929.90.3537280.980.1140.3710.92799.9
1.92-1.95100.3047290.9820.0980.320.92799.3
1.95-1.9910.20.2887160.9680.0930.3030.92699.3
1.99-2.049.90.2647250.9890.0860.2780.99699.3
2.04-2.089.10.2427290.9880.0820.2560.9899.9
2.08-2.148.70.2287270.9560.080.2420.94698.4
2.14-2.1911.20.2117290.9930.0650.2220.926100
2.19-2.2612.30.1877420.9910.0560.1951.001100
2.26-2.3312.80.1647440.9950.0490.1710.972100
2.33-2.4112.80.1547280.9940.0460.1610.948100
2.41-2.5112.70.1517370.9960.0450.1580.914100
2.51-2.6312.60.147470.990.0410.1460.927100
2.63-2.7612.40.1277390.9950.0370.1320.896100
2.76-2.9412.10.1177370.9950.0350.1220.91100
2.94-3.1611.60.1037580.9920.0320.1080.862100
3.16-3.4811.40.0977550.9950.030.1010.90599.2
3.48-3.999.10.17400.9930.0330.1060.95797.4
3.99-5.0211.70.0927810.9940.0270.0960.848100
5.02-5011.70.1058360.9870.0330.110.81499.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6wo7

6wo7


Resolution: 1.85→31.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.432 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 658 4.8 %RANDOM
Rwork0.1825 ---
obs0.1841 12918 90.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.6 Å2 / Biso mean: 19.449 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.85→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 42 134 1262
Biso mean--24.64 27.75 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181058
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.6921593
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5952458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.475141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.6921.17668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.931511
X-RAY DIFFRACTIONr_chiral_restr0.1420.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
LS refinement shellResolution: 1.853→1.901 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 28 -
Rwork0.192 680 -
all-708 -
obs--65.13 %

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