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

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Basic information

Entry
Database: PDB / ID: 6wob
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 4-diphosphoinositol pentakisphosphate (4-IP7), Mg, and Fluoride ion
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 / RNA decapping / 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 / 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 / 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-U71 / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsZong, G.N. / Wang, H.C. / Shears, B.S.
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
Water2,396133
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)44.607, 59.541, 62.470
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, 140 molecules

#2: Chemical ChemComp-U71 / (1S,2R,3S,4S,5S,6S)-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.: 133 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
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 of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM ...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 of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 2mM 4-IP7
PH range: 5.5-7.0

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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 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 30058 / % possible obs: 99.1 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.021 / Rrim(I) all: 0.062 / Χ2: 0.922 / Net I/σ(I): 10.9 / Num. measured all: 242850
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.485.80.5513390.8840.2250.5970.84991
1.48-1.56.80.48514240.9420.1850.5210.83196.5
1.5-1.537.90.42814940.960.1530.4560.85899.8
1.53-1.568.20.37814970.9680.1350.4030.86699.9
1.56-1.68.50.36114970.9710.1270.3840.86599.9
1.6-1.638.60.30214850.9810.1060.320.88499.9
1.63-1.678.70.28414870.9820.1010.3020.87399.7
1.67-1.728.50.24314990.9880.0870.2590.8799.8
1.72-1.778.50.1914970.9910.0680.2020.88799.9
1.77-1.838.30.16614880.990.060.1770.93799.7
1.83-1.898.10.13214970.9940.0480.1410.92499.8
1.89-1.977.30.10915040.9940.0420.1180.98698.9
1.97-2.066.40.07915080.9960.0330.0861.02399.7
2.06-2.179.10.0714990.9980.0240.0740.965100
2.17-2.39.10.05415180.9990.0180.0570.966100
2.3-2.488.70.04815460.9990.0170.0511.0499.9
2.48-2.738.80.04215180.9990.0140.0440.955100
2.73-3.128.40.03415430.9990.0120.0360.94399.5
3.12-3.947.10.02915540.9990.0110.0311.00899
3.94-508.50.02716640.9990.0090.0290.8999.7

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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: 1.45→31.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.232 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1343 4.9 %RANDOM
Rwork0.1602 ---
obs0.1622 26157 90.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.16 Å2 / Biso mean: 17.64 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1--5.06 Å2-0 Å20 Å2
2--2.69 Å2-0 Å2
3---2.38 Å2
Refinement stepCycle: final / Resolution: 1.45→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 46 133 1265
Biso mean--15.8 30.39 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131202
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181082
X-RAY DIFFRACTIONr_angle_refined_deg1.911.6951647
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5952516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.85120.98671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6815209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5761512
X-RAY DIFFRACTIONr_chiral_restr0.2150.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021333
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02267
X-RAY DIFFRACTIONr_rigid_bond_restr14.37132284
LS refinement shellResolution: 1.45→1.486 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.215 69 -
Rwork0.178 1223 -
obs--58.78 %
Refinement TLS params.Method: refined / Origin x: 5.907 Å / Origin y: 7.414 Å / Origin z: 13.783 Å
111213212223313233
T0.0269 Å2-0.0002 Å20.0003 Å2-0.0018 Å20.0004 Å2--0.0107 Å2
L0.1554 °2-0.082 °2-0.0072 °2-0.3643 °2-0.0196 °2--0.2237 °2
S0.0011 Å °0.0122 Å °0.005 Å °-0.0123 Å °-0.0024 Å °0.0007 Å °-0.0077 Å °0.0124 Å °0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 142
2X-RAY DIFFRACTION1A401 - 407

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