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- PDB-6jvf: Crystal structure of human apo MTH1 -

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Basic information

Entry
Database: PDB / ID: 6jvf
TitleCrystal structure of human apo MTH1
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / MTH1 / Oxidative DNA damage / 8-oxo-dGTP / Inhibitor development
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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPeng, C. / Cheng, Y.S.
CitationJournal: Bioorg.Chem. / Year: 2021
Title: Inhibitor development of MTH1 via high-throughput screening with fragment based library and MTH1 substrate binding cavity.
Authors: Peng, C. / Li, Y.H. / Yu, C.W. / Cheng, Z.H. / Liu, J.R. / Hsu, J.L. / Hsin, L.W. / Huang, C.T. / Juan, H.F. / Chern, J.W. / Cheng, Y.S.
History
DepositionApr 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
B: 7,8-dihydro-8-oxoguanine triphosphatase


Theoretical massNumber of molelcules
Total (without water)35,9432
Polymers35,9432
Non-polymers00
Water7,837435
1
A: 7,8-dihydro-8-oxoguanine triphosphatase


Theoretical massNumber of molelcules
Total (without water)17,9711
Polymers17,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7,8-dihydro-8-oxoguanine triphosphatase


Theoretical massNumber of molelcules
Total (without water)17,9711
Polymers17,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.240, 66.970, 79.921
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 17971.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.52 % / Mosaicity: 0.225 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 3.75
Details: 30% PEG6 000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 5, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 33825 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.15 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.032 / Rrim(I) all: 0.069 / Χ2: 1.069 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.794.50.48433560.8990.2450.5441.07799.6
1.79-1.864.50.36432940.9280.1850.411.08399.4
1.86-1.954.50.26233360.9660.1330.2941.07499.8
1.95-2.054.50.1933210.980.0970.2141.08399.7
2.05-2.184.50.13433690.990.0690.1511.05399.9
2.18-2.354.50.09933730.9930.0510.1121.076100
2.35-2.584.50.07733690.9950.040.0871.048100
2.58-2.964.40.06233960.9970.0330.071.08499.9
2.96-3.734.40.03434410.9990.0180.0391.08199.9
3.73-304.20.02435700.9990.0130.0281.02799.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→27.386 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2174 1933 5.9 %
Rwork0.1864 --
obs0.1883 32780 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.75 Å2 / Biso mean: 20.2542 Å2 / Biso min: 4.37 Å2
Refinement stepCycle: final / Resolution: 1.73→27.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 0 435 2911
Biso mean---33.52 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062538
X-RAY DIFFRACTIONf_angle_d0.7933428
X-RAY DIFFRACTIONf_chiral_restr0.054358
X-RAY DIFFRACTIONf_plane_restr0.006446
X-RAY DIFFRACTIONf_dihedral_angle_d12.441482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7298-1.7730.31241260.24082010213689
1.773-1.8210.25871240.22452060218492
1.821-1.87450.28641330.20582089222293
1.8745-1.9350.22471270.20462113224094
1.935-2.00420.21831360.19682170230696
2.0042-2.08440.23691420.19152186232897
2.0844-2.17920.25381410.18372229237098
2.1792-2.2940.20571410.18572224236599
2.294-2.43770.23471400.19772238237899
2.4377-2.62580.22871390.18832240237999
2.6258-2.88970.24821420.19532269241199
2.8897-3.30730.20871440.18092284242899
3.3073-4.16450.16841460.152423282474100
4.1645-27.38910.18571520.18292407255999
Refinement TLS params.Method: refined / Origin x: 15.8606 Å / Origin y: 0.4986 Å / Origin z: -10.01 Å
111213212223313233
T0.0751 Å2-0.0032 Å20.0153 Å2-0.0829 Å2-0.0016 Å2--0.0215 Å2
L1.5355 °20.1133 °20.1915 °2-0.4202 °2-0.1339 °2--0.0144 °2
S0.0321 Å °-0.1554 Å °-0.2272 Å °-0.0454 Å °-0.0166 Å °-0.0164 Å °-0.0207 Å °-0.0378 Å °-0.0077 Å °
Refinement TLS groupSelection details: all

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