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- PDB-5fsm: MTH1 substrate recognition: Complex with a methylbenzimidazolyl a... -

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Basic information

Entry
Database: PDB / ID: 5fsm
TitleMTH1 substrate recognition: Complex with a methylbenzimidazolyl acetamide.
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
ACETATE ION / N-(1-METHYLBENZIMIDAZOL-5-YL)ACETAMIDE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.67 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)18,4546
Polymers17,9711
Non-polymers4835
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.213, 66.199, 36.312
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-472-

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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-N91 / N-(1-METHYLBENZIMIDAZOL-5-YL)ACETAMIDE


Mass: 189.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11N3O
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.7→60 Å / Num. obs: 14775 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.07

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Processing

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

Resolution: 1.67→36.31 Å / Cor.coef. Fo:Fc: 0.9466 / Cor.coef. Fo:Fc free: 0.9242 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.116
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 736 4.98 %RANDOM
Rwork0.1795 ---
obs0.1811 14775 84.61 %-
Displacement parametersBiso mean: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.6491 Å20 Å20 Å2
2--0.7065 Å20 Å2
3----1.3556 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: LAST / Resolution: 1.67→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 30 176 1432
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011303HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.061769HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d443SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes193HARMONIC5
X-RAY DIFFRACTIONt_it1303HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.15
X-RAY DIFFRACTIONt_other_torsion14.6
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_contact1586SEMIHARMONIC4
LS refinement shellResolution: 1.67→1.8 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2249 73 5.42 %
Rwork0.19 1273 -
all0.192 1346 -
obs--84.61 %
Refinement TLS params.Method: refined / Origin x: 14.4079 Å / Origin y: 19.8457 Å / Origin z: 9.541 Å
111213212223313233
T-0.0026 Å20.0094 Å2-0.0001 Å2--0.0075 Å20.0108 Å2---0.0051 Å2
L0.7994 °20.2106 °20.1233 °2-0.9314 °20.0013 °2--0.7105 °2
S0.0214 Å °0.0404 Å °-0.0207 Å °0.0128 Å °0.0226 Å °0.0081 Å °-0.0068 Å °-0.0301 Å °-0.044 Å °
Refinement TLS groupSelection details: { A|3 - A|156 }

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