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- PDB-5mze: Crystal structure of mouse MTH1 with 8-oxo-dGTP -

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Basic information

Entry
Database: PDB / ID: 5mze
TitleCrystal structure of mouse MTH1 with 8-oxo-dGTP
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / substrate / complex
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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / COPPER (II) ION / DI(HYDROXYETHYL)ETHER / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNarwal, M. / Jemth, A.-S. / Helleday, T. / Stenmark, P.
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
DepositionJan 31, 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 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 7, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
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_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

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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)83,05815
Polymers80,4074
Non-polymers2,65111
Water7,350408
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8585
Polymers20,1021
Non-polymers7564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7804
Polymers20,1021
Non-polymers6793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6883
Polymers20,1021
Non-polymers5872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7313
Polymers20,1021
Non-polymers6292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.532, 139.245, 58.718
Angle α, β, γ (deg.)90.00, 107.53, 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: 20101.662 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt1, Mth1 / Production host: Escherichia coli (E. coli)
References: UniProt: P53368, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase

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Non-polymers , 5 types, 419 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium nitrate, 34% PEG 3350 and 0.01 M copper (II) chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.1→47.29 Å / Num. obs: 51831 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZR1

3zr1


Resolution: 2.1→47.29 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.556 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23867 2645 5.1 %RANDOM
Rwork0.20087 ---
obs0.20283 49154 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.89 Å2
2--1.7 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 152 408 5550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195323
X-RAY DIFFRACTIONr_bond_other_d0.0010.024861
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9817220
X-RAY DIFFRACTIONr_angle_other_deg0.7513.00511229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4035620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4823.946261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15815885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0741529
X-RAY DIFFRACTIONr_chiral_restr0.1140.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
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_it1.4142.1952477
X-RAY DIFFRACTIONr_mcbond_other1.4132.1952476
X-RAY DIFFRACTIONr_mcangle_it2.363.283098
X-RAY DIFFRACTIONr_mcangle_other2.363.2813099
X-RAY DIFFRACTIONr_scbond_it1.8622.5052846
X-RAY DIFFRACTIONr_scbond_other1.8622.5042841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1033.674119
X-RAY DIFFRACTIONr_long_range_B_refined5.24818.626002
X-RAY DIFFRACTIONr_long_range_B_other5.2518.6145997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 174 -
Rwork0.276 3549 -
obs--97.21 %

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