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- PDB-5fsi: MTH1 substrate recognition: Complex with 8-oxo-dGTP. -

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Basic information

Entry
Database: PDB / ID: 5fsi
TitleMTH1 substrate recognition: Complex with 8-oxo-dGTP.
Components7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
KeywordsHYDROLASE / NUDT1
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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / 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 / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.63 Å
AuthorsNissink, J.W.M. / Bista, M. / Breed, J. / Carter, N. / Embrey, K. / Read, J. / Phillips, C. / Winter, J.J.
CitationJournal: Plos One / Year: 2016
Title: Mth1 Substrate Recognition--an Example of Specific Promiscuity.
Authors: Nissink, J.W.M. / Bista, M. / Breed, J. / Carter, N. / Embrey, K. / Read, J. / Winter-Holt, J.J.
History
DepositionJan 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references / Refinement description

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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)18,4952
Polymers17,9711
Non-polymers5231
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.469, 66.149, 36.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2048-

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 / ...2-HYDROXY-DATP DIPHOSPHATASE / 8-OXO-DGTPASE / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1 / NUDIX MOTIF 1 / MTH1


Mass: 17971.461 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.01 Å3/Da / Density % sol: 38.74 % / Description: NONE
Crystal growDetails: 25% (W/V) PEG3350 200MM LITHIUM SULPHATE 100MM SODIUM ACETATE PH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.63→44.63 Å / Num. obs: 18433 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.6
Reflection shellResolution: 1.63→1.71 Å / Redundancy: 4 % / % possible all: 96.3

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 1.63→44.63 Å / Cor.coef. Fo:Fc: 0.9318 / Cor.coef. Fo:Fc free: 0.9265 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.098
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 915 4.96 %RANDOM
Rwork0.201 ---
obs0.2023 18433 98.56 %-
Displacement parametersBiso mean: 20.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.4317 Å20 Å20 Å2
2--0.7051 Å20 Å2
3---0.7266 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 1.63→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 32 51 1286
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011290HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.091764HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d431SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes188HARMONIC5
X-RAY DIFFRACTIONt_it1290HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.1
X-RAY DIFFRACTIONt_other_torsion14.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion158SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1456SEMIHARMONIC4
LS refinement shellResolution: 1.63→1.73 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2062 115 4.1 %
Rwork0.1854 2688 -
all0.1864 2803 -
obs--94.33 %
Refinement TLS params.Method: refined / Origin x: 14.2669 Å / Origin y: 19.7118 Å / Origin z: 9.2966 Å
111213212223313233
T-0.0507 Å20.0149 Å2-0.0079 Å2-0.0166 Å20.0104 Å2---0.0062 Å2
L0.8396 °20.481 °2-0.0194 °2-0.8634 °2-0.088 °2--0.9342 °2
S0.0394 Å °0.0149 Å °-0.0401 Å °0.0331 Å °0.007 Å °-0.003 Å °-0.012 Å °-0.0484 Å °-0.0465 Å °
Refinement TLS groupSelection details: { A|* }

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