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- PDB-6glm: Crystal structure of hMTH1 N33A in complex with LW14 in the absen... -

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Basic information

Entry
Database: PDB / ID: 6glm
TitleCrystal structure of hMTH1 N33A in complex with LW14 in the absence of acetate
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / Inhibitor / Complex / DNA repair / Fragment
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 / nucleus / metal ion binding / cytosol / cytoplasm
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
1~{H}-imidazo[4,5-b]pyridin-2-amine / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEberle, S.A. / Wiedmer, L. / Sledz, P. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
FK-16-032 Switzerland
CitationJournal: To Be Published
Title: hMTH1 N33A in complex with LW14
Authors: Eberle, S.A. / Wiedmer, L. / Sledz, P. / Caflisch, A.
History
DepositionMay 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3884
Polymers21,0621
Non-polymers3263
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.187, 60.149, 66.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

21A-425-

HOH

31A-457-

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: 21061.900 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 BL21(DE3) (bacteria)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-BU8 / 1~{H}-imidazo[4,5-b]pyridin-2-amine


Mass: 134.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.71 Å3/Da / Density % sol: 28.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5 soaked in: 0.27 M ammonium sulfate, 17% glycerol, 27% PEG4000, 20% DMSO, 10 mM compound

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 35538 / % possible obs: 96.1 % / Redundancy: 1.95 % / CC1/2: 0.999 / Rrim(I) all: 0.026 / Net I/σ(I): 26.08
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.83 % / Mean I/σ(I) obs: 9.62 / Num. unique obs: 5649 / CC1/2: 0.988 / Rrim(I) all: 0.092 / % possible all: 94.5

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C9X

4c9x


Resolution: 1.6→44.546 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.21
RfactorNum. reflection% reflection
Rfree0.2205 1969 10 %
Rwork0.1746 --
obs0.1792 19690 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 20 196 1436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051307
X-RAY DIFFRACTIONf_angle_d0.8251783
X-RAY DIFFRACTIONf_dihedral_angle_d2.3521313
X-RAY DIFFRACTIONf_chiral_restr0.055187
X-RAY DIFFRACTIONf_plane_restr0.007232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5995-1.63950.22271340.17611211X-RAY DIFFRACTION98
1.6395-1.68380.21611380.1831237X-RAY DIFFRACTION100
1.6838-1.73340.22331390.17771250X-RAY DIFFRACTION100
1.7334-1.78930.23541390.17561255X-RAY DIFFRACTION100
1.7893-1.85330.22931380.18271240X-RAY DIFFRACTION100
1.8533-1.92750.2211400.17531252X-RAY DIFFRACTION100
1.9275-2.01520.22141410.18171270X-RAY DIFFRACTION100
2.0152-2.12140.24281380.17621243X-RAY DIFFRACTION99
2.1214-2.25440.22371390.17251257X-RAY DIFFRACTION100
2.2544-2.42840.20351400.18141262X-RAY DIFFRACTION100
2.4284-2.67280.25551410.1821269X-RAY DIFFRACTION100
2.6728-3.05940.23261440.18571294X-RAY DIFFRACTION100
3.0594-3.85420.19911440.15761294X-RAY DIFFRACTION100
3.8542-44.56380.20971540.17111387X-RAY DIFFRACTION100

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