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- PDB-8i1i: Crystal structure of human MTH1(G2K/D120N mutant) in complex with... -

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Basic information

Entry
Database: PDB / ID: 8i1i
TitleCrystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 7.7
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / Nudix hydrolase
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA protection / Phosphate bond hydrolysis by NUDT proteins / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / 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-6U4 / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsNakamura, T. / Yamagata, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition.
Authors: Nakamura, T. / Koga-Ogawa, Y. / Fujimiya, K. / Chirifu, M. / Goto, M. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionJan 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-dihydro-8-oxoguanine triphosphatase
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1697
Polymers36,0852
Non-polymers1,0835
Water6,467359
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5964
Polymers18,0431
Non-polymers5533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area8440 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5733
Polymers18,0431
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.403, 47.628, 123.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 7,8-dihydro-8-oxoguanine triphosphatase / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18042.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-6U4 / [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / 2-oxo-dATP


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, tris, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→33.24 Å / Num. obs: 85778 / % possible obs: 98.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.95 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.6
Reflection shellResolution: 1.2→1.27 Å / Rmerge(I) obs: 0.461 / Num. unique obs: 13136

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.2→33.24 Å / SU ML: 0.1018 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.3437 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1633 4430 5.16 %
Rwork0.1355 81344 -
obs0.1369 85774 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 65 359 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01062993
X-RAY DIFFRACTIONf_angle_d1.34064102
X-RAY DIFFRACTIONf_chiral_restr0.0847419
X-RAY DIFFRACTIONf_plane_restr0.0094537
X-RAY DIFFRACTIONf_dihedral_angle_d17.53831146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.23311340.22532506X-RAY DIFFRACTION92.47
1.21-1.230.24691440.18952578X-RAY DIFFRACTION94.19
1.23-1.240.22751360.17152537X-RAY DIFFRACTION94.82
1.24-1.260.22911460.15872624X-RAY DIFFRACTION96.11
1.26-1.270.21941500.14862600X-RAY DIFFRACTION96.97
1.27-1.290.17021300.14212680X-RAY DIFFRACTION97.88
1.29-1.310.15721380.13652657X-RAY DIFFRACTION99.08
1.31-1.330.17491490.13152703X-RAY DIFFRACTION99.23
1.33-1.350.14541320.13032714X-RAY DIFFRACTION99.51
1.35-1.370.17241320.13732721X-RAY DIFFRACTION99.58
1.37-1.40.17591460.13452697X-RAY DIFFRACTION99.58
1.4-1.420.1871390.13542704X-RAY DIFFRACTION99.65
1.42-1.450.14561580.13732737X-RAY DIFFRACTION99.72
1.45-1.480.2011490.13122693X-RAY DIFFRACTION99.79
1.48-1.510.16911560.12452724X-RAY DIFFRACTION99.83
1.51-1.550.13351410.11692741X-RAY DIFFRACTION99.86
1.55-1.590.15021290.11622724X-RAY DIFFRACTION99.93
1.59-1.630.15491610.1142705X-RAY DIFFRACTION99.97
1.63-1.680.14121590.12242705X-RAY DIFFRACTION99.93
1.68-1.730.16781680.12282724X-RAY DIFFRACTION99.93
1.73-1.790.17191620.12522746X-RAY DIFFRACTION99.9
1.79-1.860.17351530.12252725X-RAY DIFFRACTION99.86
1.86-1.950.13251520.11822743X-RAY DIFFRACTION99.79
1.95-2.050.13741300.12122747X-RAY DIFFRACTION99.86
2.05-2.180.14021610.12032754X-RAY DIFFRACTION99.9
2.18-2.350.181470.12342788X-RAY DIFFRACTION100
2.35-2.580.15351600.14062773X-RAY DIFFRACTION99.76
2.58-2.960.16331540.14232793X-RAY DIFFRACTION99.66
2.96-3.730.14971420.13042835X-RAY DIFFRACTION99.7
3.73-33.240.17591720.16192966X-RAY DIFFRACTION99.78

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