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- PDB-6ehh: Crystal structure of mouse MTH1 mutant L116M with inhibitor TH588 -

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Basic information

Entry
Database: PDB / ID: 6ehh
TitleCrystal structure of mouse MTH1 mutant L116M with inhibitor TH588
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / Inhibitor / mutant / MTH1 / mouse
Function / homology
Function and homology information


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 / 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 / DNA protection / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / acrosomal vesicle / nuclear membrane / mitochondrial matrix / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-2GE / COPPER (II) ION / NITRATE ION / DI(HYDROXYETHYL)ETHER / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGustafsson, R. / Narwal, M. / Jemth, A.-S. / Almlof, I. / Warpman Berglund, U. / Helleday, T. / Stenmark, P.
Funding support Sweden, 10items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
the Wenner-Gren Foundation Sweden
Clas Groschinskys Foundation Sweden
Ake Wiberg Foundation Sweden
Goran Gustafsson Foundation Sweden
Swedish Children's Cancer Foundation Sweden
Swedish Pain Relief Foundation Sweden
Torsten and Ragnar Soderberg Foundation Sweden
Swedish Cancer Society Sweden
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity.
Authors: Narwal, M. / Jemth, A.S. / Gustafsson, R. / Almlof, I. / Warpman Berglund, U. / Helleday, T. / Stenmark, P.
History
DepositionSep 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / Item: _citation.year
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,01541
Polymers80,4794
Non-polymers3,53637
Water4,702261
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,98510
Polymers20,1201
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,98710
Polymers20,1201
Non-polymers8679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,25513
Polymers20,1201
Non-polymers1,13512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7888
Polymers20,1201
Non-polymers6697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.673, 142.088, 58.750
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 20119.699 Da / Num. of mol.: 4 / Mutation: L116M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt1, Mth1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P53368, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase

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Non-polymers , 7 types, 298 molecules

#2: Chemical
ChemComp-2GE / N~4~-cyclopropyl-6-(2,3-dichlorophenyl)pyrimidine-2,4-diamine


Mass: 295.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12Cl2N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium nitrate, 34% (w/v) PEG 3350, 0.01 M copper (II) chloride dihydrate, 2 mM TCEP, 10 mM TH588, 6 mM MgCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→47.4 Å / Num. obs: 35400 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.981 / Rrim(I) all: 0.271 / Net I/σ(I): 5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3577 / CC1/2: 0.429 / Rrim(I) all: 1.445 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZG

5mzg


Resolution: 2.4→47.4 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.86 / SU B: 12.186 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.296 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29924 1811 5.1 %RANDOM
Rwork0.24861 ---
obs0.25118 33560 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.3 Å2
2--1.25 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 216 261 5443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195306
X-RAY DIFFRACTIONr_bond_other_d0.0010.024728
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9787130
X-RAY DIFFRACTIONr_angle_other_deg0.805310998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1824.031258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04515881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7111528
X-RAY DIFFRACTIONr_chiral_restr0.0650.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021133
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6632.7422449
X-RAY DIFFRACTIONr_mcbond_other0.6632.7422448
X-RAY DIFFRACTIONr_mcangle_it1.2214.1083056
X-RAY DIFFRACTIONr_mcangle_other1.2214.1093057
X-RAY DIFFRACTIONr_scbond_it0.4292.8252857
X-RAY DIFFRACTIONr_scbond_other0.4292.8252857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7964.1924063
X-RAY DIFFRACTIONr_long_range_B_refined2.64429.7155488
X-RAY DIFFRACTIONr_long_range_B_other2.64429.7215489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 110 -
Rwork0.341 2381 -
obs--94.25 %

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