+Open data
-Basic information
Entry | Database: PDB / ID: 5mzg | ||||||
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Title | Crystal structure of mouse MTH1 in complex with TH588 | ||||||
Components | 7,8-dihydro-8-oxoguanine triphosphatase | ||||||
Keywords | HYDROLASE / Inhibitor / complex | ||||||
Function / homology | Function and homology information 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 / 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 / DNA protection / 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 / mitochondrial matrix / mitochondrion / extracellular space / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Narwal, M. / Jemth, A.-S. / Helleday, T. / Stenmark, P. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity. Authors: Narwal, M. / Jemth, A.S. / Gustafsson, R. / Almlof, I. / Warpman Berglund, U. / Helleday, T. / Stenmark, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mzg.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mzg.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mzg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5mzg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5mzg_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5mzg_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/5mzg ftp://data.pdbj.org/pub/pdb/validation_reports/mz/5mzg | HTTPS FTP |
-Related structure data
Related structure data | 5mzeC 5mzfC 6ehhC 3zr1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20101.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt1, Mth1 / Production host: Escherichia coli (E. coli) References: UniProt: P53368, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SCN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.7 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium thiocyanate and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→61.57 Å / Num. obs: 29434 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 3 / Num. unique all: 1775 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZR1 Resolution: 1.85→45.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.153 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.668 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→45.6 Å
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Refine LS restraints |
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