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- PDB-6glq: Crystal structure of hMTH1 N33G in complex with LW14 in the absen... -

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Basic information

Entry
Database: PDB / ID: 6glq
TitleCrystal structure of hMTH1 N33G 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: 1.601 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 N33G 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,22913
Polymers42,0962
Non-polymers1,13311
Water6,485360
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5666
Polymers21,0481
Non-polymers5185
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)21,6627
Polymers21,0481
Non-polymers6146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.698, 47.692, 124.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 21047.875 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C6H6N4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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

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: 66383 / % possible obs: 96.2 % / Redundancy: 1.97 % / CC1/2: 0.996 / Rrim(I) all: 0.059 / Net I/σ(I): 12.64
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.98 % / Mean I/σ(I) obs: 6.11 / Num. unique obs: 10878 / CC1/2: 0.975 / Rrim(I) all: 0.131 / % possible all: 97.2

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→44.517 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.5
RfactorNum. reflection% reflection
Rfree0.2101 2008 5.54 %
Rwork0.1723 --
obs0.1744 36259 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→44.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 65 360 2869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062673
X-RAY DIFFRACTIONf_angle_d0.8123644
X-RAY DIFFRACTIONf_dihedral_angle_d5.8642315
X-RAY DIFFRACTIONf_chiral_restr0.054372
X-RAY DIFFRACTIONf_plane_restr0.007475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6015-1.64150.21161490.17852357X-RAY DIFFRACTION98
1.6415-1.68590.23081340.1792422X-RAY DIFFRACTION100
1.6859-1.73550.22131400.18192410X-RAY DIFFRACTION99
1.7355-1.79150.22991470.18152412X-RAY DIFFRACTION99
1.7915-1.85560.23411350.18292409X-RAY DIFFRACTION99
1.8556-1.92990.20481360.17942406X-RAY DIFFRACTION99
1.9299-2.01770.21061460.16882406X-RAY DIFFRACTION99
2.0177-2.12410.20521450.16762421X-RAY DIFFRACTION99
2.1241-2.25720.21941420.17442445X-RAY DIFFRACTION99
2.2572-2.43140.21791410.18042447X-RAY DIFFRACTION99
2.4314-2.67610.21761450.18742463X-RAY DIFFRACTION100
2.6761-3.06320.25331470.17552484X-RAY DIFFRACTION100
3.0632-3.8590.16681450.15282515X-RAY DIFFRACTION99
3.859-44.53370.1991560.16822654X-RAY DIFFRACTION100

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