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

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Basic information

Entry
Database: PDB / ID: 6wog
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5)
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 / 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
Chem-5A3 / 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)20,3773
Polymers19,5431
Non-polymers8342
Water2,180121
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)44.802, 59.544, 62.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-5A3 / Methylenebisphosphonate inositol pentakisphosphate / {[(R)-hydroxy{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid


Mass: 738.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H21O26P7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 200 mM Li2SO4, 18% (w/v) PEG 8000, 5% (v/v) isopropanol, 100mM NaAc, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 7, 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: 27490 / % possible obs: 99.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.017 / Rrim(I) all: 0.049 / Χ2: 0.983 / Net I/σ(I): 13.5 / Num. measured all: 218627
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.537.20.64513370.9330.2480.6920.9198.7
1.53-1.557.60.53813430.9520.2040.5760.93799.6
1.55-1.587.90.51913240.9490.1940.5550.91399
1.58-1.6280.44213740.9610.1650.4730.91499
1.62-1.658.10.40513500.9590.150.4320.92799.3
1.65-1.698.10.32613530.9740.1210.3490.93399.7
1.69-1.738.10.26113570.980.0970.2790.95399.6
1.73-1.788.20.20113700.9880.0740.2140.96199.6
1.78-1.838.10.15113490.9890.0560.1620.96599.6
1.83-1.898.10.12213720.9920.0450.130.96399.7
1.89-1.968.10.09713820.9910.0360.1041.01599.6
1.96-2.048.20.07213600.9940.0270.0770.95899.9
2.04-2.138.10.06113750.9950.0230.0651.03499.9
2.13-2.248.10.05513810.9960.020.0591.16799.9
2.24-2.388.10.04713920.9960.0180.051.099100
2.38-2.568.10.0413870.9970.0150.0421.034100
2.56-2.8280.03413980.9960.0130.0361.011100
2.82-3.2380.02914250.9970.0110.0311.026100
3.23-4.077.80.02714240.9980.010.0291.02599.7
4.07-5070.02514370.9980.010.0270.87794.1

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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→27.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.527 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 1266 4.8 %RANDOM
Rwork0.1506 ---
obs0.1524 25093 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.8 Å2 / Biso mean: 17.211 Å2 / Biso min: 7.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--2.15 Å2-0 Å2
3----3.33 Å2
Refinement stepCycle: final / Resolution: 1.5→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 45 121 1252
Biso mean--31.9 34.12 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171055
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.6711604
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5792453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.3221.17668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74915203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6351511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_rigid_bond_restr6.39532228
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 93 -
Rwork0.157 1418 -
all-1511 -
obs--75.55 %
Refinement TLS params.Method: refined / Origin x: 5.9456 Å / Origin y: 7.3464 Å / Origin z: 13.7001 Å
111213212223313233
T0.0034 Å2-0.0008 Å2-0.0003 Å2-0.0025 Å2-0.0002 Å2--0.0195 Å2
L0.1044 °2-0.0311 °2-0.024 °2-0.1152 °2-0.0136 °2--0.0495 °2
S0.0004 Å °0.004 Å °0.0025 Å °0.0009 Å °0.0006 Å °-0.0045 Å °-0.0055 Å °0.0083 Å °-0.0009 Å °

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