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- PDB-3zr0: Crystal structure of human MTH1 in complex with 8-oxo-dGMP -

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Basic information

Entry
Database: PDB / ID: 3zr0
TitleCrystal structure of human MTH1 in complex with 8-oxo-dGMP
Components7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
KeywordsHYDROLASE / DNA REPAIR
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 / Phosphate bond hydrolysis by NUDT proteins ...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 / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
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
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSvensson, L.M. / Jemth, A. / Desroses, M. / Loseva, O. / Helleday, T. / Hogbom, M. / Stenmark, P.
CitationJournal: FEBS Lett. / Year: 2011
Title: Crystal Structure of Human Mth1 and the 8-Oxo-Dgmp Product Complex.
Authors: Svensson, L.M. / Jemth, A. / Desroses, M. / Loseva, O. / Helleday, T. / Hogbom, M. / Stenmark, P.
History
DepositionJun 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

Downloads & links

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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)37,1509
Polymers35,9432
Non-polymers1,2077
Water3,621201
1
A: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5274
Polymers17,9711
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6235
Polymers17,9711
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.500, 67.240, 79.990
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 / MTH1 / 8-OXO-DGTPASE / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1 / NUDIX MOTIF 1


Mass: 17971.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: NUDT1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36639, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-8OG / 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 26 % PEG6000, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0, 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→34 Å / Num. obs: 30401 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FK9

3fk9


Resolution: 1.8→51.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.644 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24616 1541 5.1 %RANDOM
Rwork0.19617 ---
obs0.19876 28783 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→51.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 73 201 2750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222610
X-RAY DIFFRACTIONr_bond_other_d0.0010.021781
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.9873538
X-RAY DIFFRACTIONr_angle_other_deg1.01734314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87524.264129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0521.51506
X-RAY DIFFRACTIONr_mcbond_other0.3311.5626
X-RAY DIFFRACTIONr_mcangle_it1.81422425
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.26831104
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0444.51113
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 109 -
Rwork0.25 2089 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57640.7827-0.36961.8031-0.22250.8730.0298-0.1069-0.03720.0815-0.06720.0133-0.03350.02970.03750.0872-0.0019-0.01120.0598-0.00160.0128-0.041-11.169-11.12
27.32180.17771.81171.85530.05361.00280.1093-0.69291.1497-0.024-0.1232-0.11440.0778-0.07650.01390.0743-0.02630.03970.143-0.1550.314128.22911.373-8.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 156
2X-RAY DIFFRACTION2B2 - 156

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