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- PDB-6woi: Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) ... -

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Basic information

Entry
Database: PDB / ID: 6woi
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-Diphosphoinositol pentakisphosphate, Mg, and Fluoride ion, presoaked with 1,5-IP8, Mg and Fluoride for 30 seconds
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / phosphatase / nudix / catalysis mechanism / Substrate Specificity / inositol / inositol pyrophosphate
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-O81 / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsZong, G.N. / Wang, H.C. / 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: 2021
Title: New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1.
Authors: Zong, G. / Jork, N. / Hostachy, S. / Fiedler, D. / Jessen, H.J. / Shears, S.B. / Wang, H.
History
DepositionApr 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,4468
Polymers19,5431
Non-polymers9037
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.503, 59.608, 62.353
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: 19542.922 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, 138 molecules

#2: Chemical ChemComp-O81 / (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate


Mass: 740.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H19O27P7 / 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.: 2 / 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.: 131 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution 400 mM LiCl, 30% (w/v) PEG 8000, 20% (v/v) isopropanol, 100mM ...Details: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution 400 mM LiCl, 30% (w/v) PEG 8000, 20% (v/v) isopropanol, 100mM NaAc, pH 4.5, 20 mM MgCl2 and 80 mM NaF in present of 2mM 1,5-IP8, and transferred into 400 mM LiCl, 30% (w/v) PEG 8000, 20% (v/v) isopropanol, 100mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF for 30 second.

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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: Jul 10, 2019
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: 28143 / % possible obs: 99 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.024 / Rrim(I) all: 0.073 / Χ2: 0.935 / Net I/σ(I): 10.5 / Num. measured all: 237334
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.537.30.56213590.9050.2070.6020.88297.1
1.53-1.557.50.51313650.9170.1860.5480.88998.1
1.55-1.5880.52413780.9350.190.560.88299.3
1.58-1.6280.49613840.9340.180.530.90199.7
1.62-1.658.30.44714040.940.1630.4780.88699.7
1.65-1.698.50.40714090.950.1490.4350.87999.9
1.69-1.738.40.37513910.9510.1380.4020.86799.9
1.73-1.788.40.30314040.9740.1130.3250.89299.6
1.78-1.838.40.25713930.9750.0960.2750.90899.8
1.83-1.898.20.21814010.9790.0820.2340.89599.1
1.89-1.967.70.1714030.9830.0660.1830.89399
1.96-2.047.10.14213880.9840.0580.1540.90298.5
2.04-2.139.20.12214140.9950.0430.130.90599.8
2.13-2.249.60.09814050.9960.0340.1040.9599.7
2.24-2.389.50.08314240.9960.0290.0880.9999.9
2.38-2.569.40.06914250.9960.0240.0730.97599.9
2.56-2.829.30.05614290.9970.0190.0591.01299.6
2.82-3.238.80.04514330.9970.0160.0481.08498.8
3.23-4.077.90.03414130.9980.0120.0361.11295.7
4.07-509.10.02915210.9980.010.0310.93796.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→31.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.814 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1673 1245 4.8 %RANDOM
Rwork0.1449 ---
obs0.146 24545 90.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.19 Å2 / Biso mean: 17.432 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å2-0 Å20 Å2
2--2.33 Å2-0 Å2
3----3.65 Å2
Refinement stepCycle: final / Resolution: 1.5→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 46 131 1263
Biso mean--28.52 33.15 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131184
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181067
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.71622
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5942483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02921.30469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30215206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4981511
X-RAY DIFFRACTIONr_chiral_restr0.1310.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
X-RAY DIFFRACTIONr_rigid_bond_restr8.16832251
LS refinement shellResolution: 1.501→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 79 -
Rwork0.165 1305 -
all-1384 -
obs--67.45 %
Refinement TLS params.Method: refined / Origin x: 6.0818 Å / Origin y: 7.2001 Å / Origin z: 13.9527 Å
111213212223313233
T0.029 Å2-0.0001 Å20.0002 Å2-0.0047 Å20 Å2--0.0371 Å2
L0.2034 °2-0.0647 °2-0.0177 °2-0.2226 °2-0.0105 °2--0.1104 °2
S0.0005 Å °0.0092 Å °0.0007 Å °-0.0057 Å °-0.0018 Å °-0.0049 Å °-0.0046 Å °0.0205 Å °0.0013 Å °

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