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

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Basic information

Entry
Database: PDB / ID: 6woc
TitleDiphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol pentakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 1min in the absence of Fluoride.
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / phosphatase / nudix / catalysis mechanism / Substrate Specificity / inositol / inositol pyrophosphate
Function / homology
Function and homology information


diphosphoinositol polyphosphate catabolic process / diadenosine polyphosphate catabolic process / bis(5'-adenosyl)-hexaphosphatase activity / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diadenosine hexaphosphate catabolic process / endopolyphosphatase activity / diadenosine pentaphosphate catabolic process / RNA decapping / diphosphoinositol polyphosphate metabolic process / bis(5'-adenosyl)-pentaphosphatase activity ...diphosphoinositol polyphosphate catabolic process / diadenosine polyphosphate catabolic process / bis(5'-adenosyl)-hexaphosphatase activity / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diadenosine hexaphosphate catabolic process / endopolyphosphatase activity / diadenosine pentaphosphate catabolic process / RNA decapping / diphosphoinositol polyphosphate metabolic process / bis(5'-adenosyl)-pentaphosphatase activity / inositol diphosphate pentakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / Synthesis of pyrophosphates in the cytosol / m7G(5')pppN diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cell-cell signaling / magnesium ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / NUDIX hydrolase domain / Nudix hydrolase domain profile. / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Chem-I7P / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4277
Polymers19,5431
Non-polymers8846
Water2,918162
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)45.708, 59.611, 62.581
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-I7P / (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate / 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate


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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
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 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, 80 mM NaF, 20 mM MgCl2 in present of 2mM 5-IP7 for 2 days, and transferred into 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 for 1min.

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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: 1.35→50 Å / Num. obs: 37111 / % possible obs: 97 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.019 / Rrim(I) all: 0.058 / Χ2: 0.93 / Net I/σ(I): 12.7 / Num. measured all: 348699
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.377.60.53615280.9480.1940.5720.86781.5
1.37-1.47.80.47715950.9720.170.5080.88684.9
1.4-1.437.90.49716930.9710.1750.5290.89690.3
1.43-1.457.80.46318190.970.1650.4930.90195.8
1.45-1.497.70.39418060.9680.1430.4210.90496.2
1.49-1.529.60.34218980.9870.1140.3610.90299.7
1.52-1.5610.10.26918690.9890.0880.2840.89199.8
1.56-1.610.30.26518870.9910.0860.2790.92599.5
1.6-1.6510.20.20618820.9940.0670.2170.90899.6
1.65-1.710.10.1719000.9950.0560.1790.90499.5
1.7-1.76100.14518910.9950.0480.1530.9199.4
1.76-1.839.80.10718730.9950.0360.1130.92199.3
1.83-1.929.40.08718940.9960.030.0930.94199.3
1.92-2.028.20.06818560.9960.0250.0730.94197.9
2.02-2.1410.10.05719310.9980.0190.060.92799.9
2.14-2.3110.70.04919190.9980.0160.0520.98599.9
2.31-2.5410.60.04219320.9980.0140.0450.94499.9
2.54-2.9110.20.0419360.9980.0130.0421.01999.5
2.91-3.6690.03619300.9960.0130.0391.01197.7
3.66-509.80.03520720.9970.0120.0370.94898.7

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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: 1.35→31.4 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.618 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1638 1695 5 %RANDOM
Rwork0.138 ---
obs0.1393 32263 88.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.76 Å2 / Biso mean: 16.805 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å2-0 Å20 Å2
2--2.52 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.35→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 45 162 1293
Biso mean--22.41 33.04 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131193
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181078
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6931636
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5942509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0135147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.59221.30469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.28815208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6051511
X-RAY DIFFRACTIONr_chiral_restr0.2180.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
X-RAY DIFFRACTIONr_rigid_bond_restr5.35632271
LS refinement shellResolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 83 -
Rwork0.172 1591 -
all-1674 -
obs--59.83 %
Refinement TLS params.Method: refined / Origin x: 5.9448 Å / Origin y: 7.1252 Å / Origin z: 13.8261 Å
111213212223313233
T0.0234 Å2-0.0005 Å2-0.0003 Å2-0.0027 Å20 Å2--0.0245 Å2
L0.1158 °2-0.0591 °2-0.0176 °2-0.1786 °2-0.0249 °2--0.077 °2
S0.0003 Å °0.0079 Å °0.002 Å °-0.0048 Å °-0.0012 Å °-0.0049 Å °-0.0007 Å °0.0102 Å °0.0009 Å °

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