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- PDB-8i1c: Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo... -

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Basic information

Entry
Database: PDB / ID: 8i1c
TitleCrystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 9.1
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 / 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
Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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

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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)36,2717
Polymers36,0872
Non-polymers1845
Water6,774376
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1134
Polymers18,0441
Non-polymers693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area8290 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 area130 Å2
ΔGint-10 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.799, 47.960, 123.627
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.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
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: 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: 1.4→30.63 Å / Num. obs: 53968 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.94 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 58.6
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.139 / Num. unique obs: 5040

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→30.63 Å / SU ML: 0.1255 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1188 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1844 2733 5.07 %
Rwork0.1525 51167 -
obs0.1541 53900 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 10 376 2909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072777
X-RAY DIFFRACTIONf_angle_d0.93823772
X-RAY DIFFRACTIONf_chiral_restr0.0813389
X-RAY DIFFRACTIONf_plane_restr0.0079500
X-RAY DIFFRACTIONf_dihedral_angle_d13.58351048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.19471200.14982280X-RAY DIFFRACTION89.59
1.42-1.450.22891180.1462463X-RAY DIFFRACTION96.06
1.45-1.480.18371310.13742541X-RAY DIFFRACTION98.06
1.48-1.510.20881360.13082523X-RAY DIFFRACTION99.89
1.51-1.540.17491490.12512562X-RAY DIFFRACTION100
1.54-1.580.16981570.12672521X-RAY DIFFRACTION100
1.58-1.620.16831520.12762535X-RAY DIFFRACTION100
1.62-1.660.19811310.13072567X-RAY DIFFRACTION100
1.66-1.710.17531550.13112553X-RAY DIFFRACTION100
1.71-1.760.20441450.13332534X-RAY DIFFRACTION100
1.76-1.830.16971330.13752584X-RAY DIFFRACTION100
1.83-1.90.17081340.13422584X-RAY DIFFRACTION100
1.9-1.990.181210.13392586X-RAY DIFFRACTION100
1.99-2.090.15551340.14142593X-RAY DIFFRACTION100
2.09-2.220.17821200.14662589X-RAY DIFFRACTION100
2.22-2.390.16061130.15662640X-RAY DIFFRACTION100
2.39-2.630.19421520.17592602X-RAY DIFFRACTION99.96
2.63-3.020.20971500.18942628X-RAY DIFFRACTION99.96
3.02-3.80.17551290.15242654X-RAY DIFFRACTION99.71
3.8-30.630.19551530.17332628X-RAY DIFFRACTION94.3

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