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- PDB-8i8t: Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo... -

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Basic information

Entry
Database: PDB / ID: 8i8t
TitleCrystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dAMP and Mn2+
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 / cytoplasm / cytosol
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
2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE / : / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.22 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
DepositionFeb 5, 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)37,0018
Polymers36,0872
Non-polymers9146
Water7,891438
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5565
Polymers18,0441
Non-polymers5124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-9 kcal/mol
Surface area8250 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4463
Polymers18,0441
Non-polymers4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-4 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.476, 47.512, 124.061
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-IGU / 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 35.19 %
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: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→44.37 Å / Num. obs: 80949 / % possible obs: 98.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 15.24 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 38.9
Reflection shellResolution: 1.22→1.24 Å / Rmerge(I) obs: 0.514 / Num. unique obs: 3847

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.22→44.37 Å / SU ML: 0.1174 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.7156 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1799 4054 5.01 %
Rwork0.1498 76825 -
obs0.1513 80879 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.22→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 50 438 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523036
X-RAY DIFFRACTIONf_angle_d0.86854136
X-RAY DIFFRACTIONf_chiral_restr0.0777419
X-RAY DIFFRACTIONf_plane_restr0.0064549
X-RAY DIFFRACTIONf_dihedral_angle_d16.77971157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.240.26621390.22942359X-RAY DIFFRACTION89.95
1.24-1.250.241420.20892579X-RAY DIFFRACTION95.81
1.25-1.270.23911370.19482528X-RAY DIFFRACTION96.38
1.27-1.280.21761140.17742618X-RAY DIFFRACTION96.71
1.28-1.30.19341430.17342575X-RAY DIFFRACTION97
1.3-1.320.21781340.16942599X-RAY DIFFRACTION97.33
1.32-1.340.19931330.15822601X-RAY DIFFRACTION97.68
1.34-1.360.19381350.15532623X-RAY DIFFRACTION97.59
1.36-1.380.20341380.14982589X-RAY DIFFRACTION97.92
1.38-1.410.21921510.14742606X-RAY DIFFRACTION97.87
1.41-1.430.2061420.14242607X-RAY DIFFRACTION97.97
1.43-1.460.20051380.13952618X-RAY DIFFRACTION98.11
1.46-1.490.18331220.13852661X-RAY DIFFRACTION98.44
1.49-1.520.18631340.13792625X-RAY DIFFRACTION98.54
1.52-1.560.19231310.13292647X-RAY DIFFRACTION98.23
1.56-1.60.1771340.13262665X-RAY DIFFRACTION98.9
1.6-1.640.15651390.1322642X-RAY DIFFRACTION98.62
1.64-1.690.17781320.13332659X-RAY DIFFRACTION98.8
1.69-1.740.17721530.13632670X-RAY DIFFRACTION99.37
1.74-1.80.18961550.13932656X-RAY DIFFRACTION99.26
1.8-1.880.17331250.14342697X-RAY DIFFRACTION99.68
1.88-1.960.17791480.13592704X-RAY DIFFRACTION99.72
1.96-2.060.19241570.14052680X-RAY DIFFRACTION99.79
2.06-2.190.16641410.14262712X-RAY DIFFRACTION99.79
2.19-2.360.16951530.1542715X-RAY DIFFRACTION99.9
2.36-2.60.19021380.16192741X-RAY DIFFRACTION99.86
2.6-2.980.18511380.16982757X-RAY DIFFRACTION99.97
2.98-3.750.1591530.13932779X-RAY DIFFRACTION99.86
3.75-44.370.17411550.15592913X-RAY DIFFRACTION99.16

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