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- PDB-8i1h: Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo... -

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Basic information

Entry
Database: PDB / ID: 8i1h
TitleCrystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP at pH 9.7
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 / 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
Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.18 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)36,3407
Polymers36,0872
Non-polymers2535
Water6,089338
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1824
Polymers18,0441
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area8410 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1593
Polymers18,0441
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.979, 47.995, 123.977
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 35.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, caps, 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: 1.18→33.2 Å / Num. obs: 90653 / % possible obs: 98.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.22 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.2
Reflection shellResolution: 1.18→1.25 Å / Rmerge(I) obs: 0.394 / Num. unique obs: 13801

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.18→33.2 Å / SU ML: 0.0974 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.0432 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1656 4472 4.93 %
Rwork0.1353 86173 -
obs0.1368 90645 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.23 Å2
Refinement stepCycle: LAST / Resolution: 1.18→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 15 338 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022926
X-RAY DIFFRACTIONf_angle_d1.02783990
X-RAY DIFFRACTIONf_chiral_restr0.0781411
X-RAY DIFFRACTIONf_plane_restr0.0088534
X-RAY DIFFRACTIONf_dihedral_angle_d13.40981120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.2521230.20262560X-RAY DIFFRACTION88.81
1.19-1.20.22441370.1722709X-RAY DIFFRACTION93.87
1.2-1.220.22831400.16162731X-RAY DIFFRACTION95.57
1.22-1.230.2061500.14872784X-RAY DIFFRACTION96.64
1.23-1.250.18511370.13552759X-RAY DIFFRACTION97.18
1.25-1.270.151380.12882837X-RAY DIFFRACTION98.28
1.27-1.290.15641390.12382848X-RAY DIFFRACTION99.04
1.29-1.310.17341590.12572842X-RAY DIFFRACTION99.37
1.31-1.330.16241600.11852869X-RAY DIFFRACTION99.7
1.33-1.350.1811350.12222885X-RAY DIFFRACTION99.7
1.35-1.370.1651340.1232859X-RAY DIFFRACTION99.87
1.37-1.40.17291270.122913X-RAY DIFFRACTION99.8
1.4-1.420.16411310.12512880X-RAY DIFFRACTION99.93
1.42-1.450.16761450.1252911X-RAY DIFFRACTION99.87
1.45-1.480.18691350.11592905X-RAY DIFFRACTION99.93
1.48-1.520.15331480.10752842X-RAY DIFFRACTION99.9
1.52-1.560.14231300.10762941X-RAY DIFFRACTION99.93
1.56-1.60.13251650.1082875X-RAY DIFFRACTION99.87
1.6-1.640.15681620.10962875X-RAY DIFFRACTION99.93
1.64-1.70.14471510.11552912X-RAY DIFFRACTION100
1.7-1.760.16231800.11562872X-RAY DIFFRACTION99.97
1.76-1.830.16731740.11732853X-RAY DIFFRACTION99.97
1.83-1.910.14051540.11572925X-RAY DIFFRACTION99.9
1.91-2.010.16171280.11332936X-RAY DIFFRACTION99.84
2.01-2.140.12891890.11642874X-RAY DIFFRACTION99.9
2.14-2.30.13251500.12212957X-RAY DIFFRACTION99.97
2.3-2.540.16221830.13712907X-RAY DIFFRACTION99.9
2.54-2.90.16871500.15292968X-RAY DIFFRACTION99.94
2.9-3.660.17261550.14452996X-RAY DIFFRACTION99.84
3.66-33.20.19921630.17273148X-RAY DIFFRACTION99.79

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