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- PDB-8i18: Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo... -

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Basic information

Entry
Database: PDB / ID: 8i18
TitleCrystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP 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 / Phosphate bond hydrolysis by NUDT proteins ...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 / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / 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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 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)37,2037
Polymers36,0872
Non-polymers1,1155
Water7,440413
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6134
Polymers18,0441
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area8280 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5903
Polymers18,0441
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.442, 47.754, 124.159
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 / MutT homologue-1 / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked ...MutT homologue-1 / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18043.590 Da / Num. of mol.: 2 / Fragment: UNP residues 42-197
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-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / 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.: 413 / 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: 1.91 Å3/Da / Density % sol: 35.52 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→33.29 Å / Num. obs: 110402 / % possible obs: 98 % / Redundancy: 7.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 58.8
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.232 / Num. unique obs: 9630

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→33.29 Å / SU ML: 0.0802 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.2714 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1693 5541 5.01 %
Rwork0.1448 104964 -
obs0.1461 110402 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.31 Å2
Refinement stepCycle: LAST / Resolution: 1.1→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 67 413 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962834
X-RAY DIFFRACTIONf_angle_d1.37543866
X-RAY DIFFRACTIONf_chiral_restr0.0842398
X-RAY DIFFRACTIONf_plane_restr0.0091496
X-RAY DIFFRACTIONf_dihedral_angle_d16.82511077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.18821470.16752777X-RAY DIFFRACTION78.67
1.11-1.130.18661440.16583118X-RAY DIFFRACTION87.95
1.13-1.140.17631580.16573252X-RAY DIFFRACTION91.77
1.14-1.150.19351970.17283407X-RAY DIFFRACTION97.2
1.15-1.170.2151940.17553478X-RAY DIFFRACTION98.16
1.17-1.180.2251900.18923439X-RAY DIFFRACTION98.13
1.18-1.20.22531690.18553471X-RAY DIFFRACTION98.33
1.2-1.220.20821680.16313522X-RAY DIFFRACTION98.51
1.22-1.240.16491760.14043468X-RAY DIFFRACTION98.65
1.24-1.260.17091840.13463539X-RAY DIFFRACTION98.81
1.26-1.280.1391710.11813493X-RAY DIFFRACTION98.81
1.28-1.30.15941690.11953512X-RAY DIFFRACTION99.06
1.3-1.330.15161820.11763565X-RAY DIFFRACTION99.23
1.33-1.360.16521670.11493498X-RAY DIFFRACTION99.16
1.36-1.390.16911870.12083516X-RAY DIFFRACTION99.33
1.39-1.420.14562040.11773507X-RAY DIFFRACTION99.44
1.42-1.450.1611960.123554X-RAY DIFFRACTION99.58
1.45-1.490.13991910.11523554X-RAY DIFFRACTION99.65
1.49-1.540.12862200.11233487X-RAY DIFFRACTION99.68
1.54-1.590.14461830.11343591X-RAY DIFFRACTION99.84
1.59-1.640.14991900.1133524X-RAY DIFFRACTION99.87
1.64-1.710.14971940.12133599X-RAY DIFFRACTION99.97
1.71-1.790.1561950.12463553X-RAY DIFFRACTION99.95
1.79-1.880.14561780.1323583X-RAY DIFFRACTION100
1.88-20.14841790.13043606X-RAY DIFFRACTION100
2-2.150.15452030.13593604X-RAY DIFFRACTION100
2.15-2.370.15711850.13963644X-RAY DIFFRACTION100
2.37-2.710.17532090.16233625X-RAY DIFFRACTION100
2.71-3.420.19392160.16553666X-RAY DIFFRACTION100
3.42-33.290.19321950.17433812X-RAY DIFFRACTION98.82

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