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- PDB-3zr1: Crystal structure of human MTH1 -

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Basic information

Entry
Database: PDB / ID: 3zr1
TitleCrystal structure of human MTH1
Components7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
KeywordsHYDROLASE
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 / DNA protection / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity ...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 / DNA protection / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 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
ACETATE ION / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)36,4458
Polymers35,9432
Non-polymers5026
Water3,171176
1
A: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3195
Polymers17,9711
Non-polymers3474
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)18,1273
Polymers17,9711
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.520, 67.080, 80.130
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 / 8-OXO-DGTPASE / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1 / NUDIX MOTIF 1 / MTH1


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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / 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 / 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: 1.9→34 Å / Num. obs: 25933 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.3 / % possible all: 97.8

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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: 1.9→51.44 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.446 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24455 1311 5.1 %RANDOM
Rwork0.19067 ---
obs0.19339 24313 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.576 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---0.43 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 28 176 2680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222560
X-RAY DIFFRACTIONr_bond_other_d0.0010.021759
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9633458
X-RAY DIFFRACTIONr_angle_other_deg1.27934262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74224.264129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60715439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4011515
X-RAY DIFFRACTIONr_chiral_restr0.1210.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212832
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02543
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_it1.0381.51512
X-RAY DIFFRACTIONr_mcbond_other0.2271.5626
X-RAY DIFFRACTIONr_mcangle_it1.9222429
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.37131048
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4594.51029
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 94 -
Rwork0.253 1737 -
obs--97.14 %
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)
10.84430.336-0.17951.20130.01190.6536-0.0129-0.0258-0.00880.0284-0.02930.01680.01180.0270.04210.10210.0012-0.01530.07240.00540.03040.101-11.14-11.079
25.88260.19721.30961.1810.06380.59770.1235-0.27490.722-0.059-0.108-0.07860.1214-0.0398-0.01550.1137-0.01580.01450.0904-0.0590.217828.28810.847-8.908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 156
2X-RAY DIFFRACTION2B2 - 156

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