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- PDB-5fsl: MTH1 substrate recognition: Complex with a methylaminopurinone -

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Basic information

Entry
Database: PDB / ID: 5fsl
TitleMTH1 substrate recognition: Complex with a methylaminopurinone
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 / 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
9-METHYL-2-(METHYLAMINO)-1H-PURIN-6-ONE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.24 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 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references / Refinement description
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,2473
Polymers17,9711
Non-polymers2752
Water1,874104
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

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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: 17971.461 Da / Num. of mol.: 1 / Fragment: YES, 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-UAN / 9-METHYL-2-(METHYLAMINO)-1H-PURIN-6-ONE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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: 1.25→60 Å / Num. obs: 35440 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 13.47 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22

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Processing

SoftwareName: BUSTER / Version: 2.11.6 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.24→11.76 Å / Cor.coef. Fo:Fc: 0.9528 / Cor.coef. Fo:Fc free: 0.9537 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.054
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1704 4.82 %RANDOM
Rwork0.2015 ---
obs0.202 35353 85.41 %-
Displacement parametersBiso mean: 15.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.8224 Å20 Å20 Å2
2---0.6722 Å20 Å2
3----0.1502 Å2
Refine analyzeLuzzati coordinate error obs: 0.164 Å
Refinement stepCycle: LAST / Resolution: 1.24→11.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 18 104 1319
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011275HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.051740HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d417SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes188HARMONIC5
X-RAY DIFFRACTIONt_it1275HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.99
X-RAY DIFFRACTIONt_other_torsion13.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion156SEMIHARMONIC5
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_contact1483SEMIHARMONIC4
LS refinement shellResolution: 1.24→1.28 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2095 58 4.57 %
Rwork0.2179 1210 -
all0.2175 1268 -
obs--85.41 %
Refinement TLS params.Method: refined / Origin x: 14.3047 Å / Origin y: 19.6096 Å / Origin z: 9.3227 Å
111213212223313233
T-0.0027 Å20.0066 Å2-0.006 Å2-0.0039 Å20.0008 Å2---0.0082 Å2
L0.6949 °20.2127 °20.0648 °2-0.5827 °2-0.0708 °2--0.5413 °2
S0.0265 Å °0.0196 Å °-0.0454 Å °0.0067 Å °0.0088 Å °-0.0004 Å °-0.0027 Å °-0.0154 Å °-0.0353 Å °
Refinement TLS groupSelection details: { A|* }

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