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- PDB-8i1c: Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i1c | |||||||||
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Title | Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 9.1 | |||||||||
![]() | 7,8-dihydro-8-oxoguanine triphosphatase | |||||||||
![]() | HYDROLASE / Nudix hydrolase | |||||||||
Function / homology | ![]() 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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nakamura, T. / Yamagata, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Authors: Nakamura, T. / Koga-Ogawa, Y. / Fujimiya, K. / Chirifu, M. / Goto, M. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.7 KB | Display | ![]() |
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PDB format | ![]() | 119.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 760.8 KB | Display | ![]() |
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Full document | ![]() | 761.8 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i18C ![]() 8i19C ![]() 8i1aC ![]() 8i1dC ![]() 8i1eC ![]() 8i1fC ![]() 8i1gC ![]() 8i1hC ![]() 8i1iC ![]() 8i1jC ![]() 8i8sC ![]() 8i8tC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18043.590 Da / Num. of mol.: 2 / Fragment: UNP residues 42-197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, caps, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30.63 Å / Num. obs: 53968 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.94 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 58.6 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.139 / Num. unique obs: 5040 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30.63 Å
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Refine LS restraints |
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LS refinement shell |
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