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- PDB-7esf: The Crystal Structure of human MTH1 from Biortus -

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Basic information

Entry
Database: PDB / ID: 7esf
TitleThe Crystal Structure of human MTH1 from Biortus
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / catalytic activity / pyrophosphatase activity / hydrolase activity
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
DI(HYDROXYETHYL)ETHER / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWang, F. / Cheng, W. / Shang, H. / Wang, R. / Zhang, B. / Tian, F.
CitationJournal: To Be Published
Title: The Crystal Structure of human MTH1 from Biortus
Authors: Wang, F. / Cheng, W. / Shang, H. / Wang, R. / Zhang, B. / Tian, F.
History
DepositionMay 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,3723
Polymers20,0721
Non-polymers3002
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint6 kcal/mol
Surface area8480 Å2
Unit cell
Length a, b, c (Å)36.276, 60.533, 66.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-405-

HOH

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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: 20071.709 Da / Num. of mol.: 1
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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.81 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M Citric Acid pH 4.0, 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.5212 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5212 Å / Relative weight: 1
ReflectionResolution: 1.55→44.653 Å / Num. obs: 21691 / % possible obs: 99.4 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 28.3
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.427 / Num. unique obs: 1011

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q93

3q93


Resolution: 1.55→44.653 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.188 / SU B: 1.305 / SU ML: 0.049 / Average fsc free: 0.9401 / Average fsc work: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.215 1045 4.826 %
Rwork0.1885 20610 -
all0.19 --
obs-21655 99.267 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.594 Å20 Å2-0 Å2
2---0.516 Å20 Å2
3----0.078 Å2
Refinement stepCycle: LAST / Resolution: 1.55→44.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 20 113 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131312
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171208
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6441768
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5792810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9375157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52622.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17115225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.806158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.2170.2188
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21087
X-RAY DIFFRACTIONr_nbtor_refined0.180.2599
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.217
X-RAY DIFFRACTIONr_nbd_other0.2420.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.217
X-RAY DIFFRACTIONr_mcbond_it1.6031.384619
X-RAY DIFFRACTIONr_mcbond_other1.6011.383618
X-RAY DIFFRACTIONr_mcangle_it2.2992.078773
X-RAY DIFFRACTIONr_mcangle_other2.2982.079774
X-RAY DIFFRACTIONr_scbond_it2.8321.781692
X-RAY DIFFRACTIONr_scbond_other2.831.783693
X-RAY DIFFRACTIONr_scangle_it4.2322.507993
X-RAY DIFFRACTIONr_scangle_other4.232.51994
X-RAY DIFFRACTIONr_lrange_it5.31316.731372
X-RAY DIFFRACTIONr_lrange_other5.25916.3831354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.55-1.590.313820.26914410.27115880.880.91895.90680.269
1.59-1.6340.213750.20814570.20815340.9390.94899.86960.208
1.634-1.6810.228720.17214290.17515030.9430.95899.86690.172
1.681-1.7330.203620.16714010.16914660.9560.9699.79540.167
1.733-1.7890.223610.17113530.17314160.940.9699.85880.171
1.789-1.8520.259680.19213030.19513730.9160.94299.85430.192
1.852-1.9220.261610.18612660.18913280.9250.94399.92470.186
1.922-20.225580.18112100.18312710.9490.95399.7640.181
2-2.0890.217490.1911780.19112370.9430.95499.19160.19
2.089-2.1910.205580.18110940.18311670.9510.96298.71470.181
2.191-2.3090.148540.18610700.18411340.9670.96599.11820.186
2.309-2.4490.198550.1779990.17910710.950.96298.41270.177
2.449-2.6170.219550.1879470.18910160.9440.95498.6220.187
2.617-2.8260.216450.1978710.1989220.950.94899.34920.197
2.826-3.0940.188440.1898250.1898720.9520.94899.6560.189
3.094-3.4580.205500.1817490.1838030.9490.95499.50190.181
3.458-3.9890.181360.1646740.1657100.9630.9661000.164
3.989-4.8750.191250.1665780.1676040.9730.96899.83440.166
4.875-6.8540.298210.2444760.2464970.9330.9491000.244
6.854-44.6530.358140.2632890.2683030.9370.9341000.263

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