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Yorodumi- PDB-6glu: Crystal structure of hMTH1 D120N in complex with LW14 in the pres... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6glu | ||||||
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Title | Crystal structure of hMTH1 D120N in complex with LW14 in the presence of acetate | ||||||
Components | 7,8-dihydro-8-oxoguanine triphosphatase | ||||||
Keywords | HYDROLASE / Inhibitor / Complex / DNA repair / Fragment | ||||||
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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Eberle, S.A. / Wiedmer, L. / Sledz, P. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: hMTH1 D120N in complex with LW14 Authors: Eberle, S.A. / Wiedmer, L. / Sledz, P. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6glu.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6glu.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 6glu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/6glu ftp://data.pdbj.org/pub/pdb/validation_reports/gl/6glu | HTTPS FTP |
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-Related structure data
Related structure data | 4c9xS S: Starting model for refinement |
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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: 21103.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase |
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#2: Chemical | ChemComp-BU8 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density % sol: 27.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5 soaked in: 27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5, 20% DMSO, 10 mM compound |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 27698 / % possible obs: 90 % / Redundancy: 1.91 % / CC1/2: 0.999 / Rrim(I) all: 0.029 / Net I/σ(I): 24.19 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 9.04 / Num. unique obs: 4950 / CC1/2: 0.989 / Rrim(I) all: 0.088 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C9X Resolution: 1.7→44.447 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.447 Å
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Refine LS restraints |
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LS refinement shell |
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