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- PDB-8dvp: Glycosylase MutY variant N146S in complex with DNA containing d(8... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dvp | |||||||||||||||
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Title | Glycosylase MutY variant N146S in complex with DNA containing d(8-oxo-G) paired with substrate purine | |||||||||||||||
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![]() | HYDROLASE/DNA / Protein-DNA complex / DNA repair / Base Excision Repair / HYDROLASE / HYDROLASE-DNA complex | |||||||||||||||
Function / homology | ![]() adenine glycosylase / adenine/guanine mispair binding / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Demir, M. / Russelburg, L.P. / Horvath, M.P. / David, S.S. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism. Authors: Demir, M. / Russelburg, L.P. / Lin, W.J. / Trasvina-Arenas, C.H. / Huang, B. / Yuen, P.K. / Horvath, M.P. / David, S.S. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.6 KB | Display | ![]() |
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PDB format | ![]() | 194.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dvyC ![]() 8dw0C ![]() 8dw4C ![]() 8dw7C ![]() 6u7tS S: Starting model for refinement 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41746.574 Da / Num. of mol.: 1 / Mutation: N146S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET28A / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3423.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3309.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 185 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SF4 / | ||
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#5: Chemical | ChemComp-ACT / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: PEG 4000, calcium acetate, ethylene glycol, Tris.HCl, b-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 6, 2019 |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11585 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→73.49 Å / Num. obs: 130827 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.15 |
Reflection shell | Resolution: 1.54→1.58 Å / Num. unique obs: 9558 / CC1/2: 0.146 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6U7T Resolution: 1.54→73.49 Å / SU ML: 0.2817 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.283 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→73.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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