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Open data
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Basic information
Entry | Database: PDB / ID: 3sat | ||||||
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Title | MUTM Slanted complex 6 with R112A mutation | ||||||
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![]() | HYDROLASE/DNA / DNA GLYCOSYLASE / DNA REPAIR / DAMAGE SEARCH / TRANSLOCATION / DISULFIDE CROSSLINKING / DNA DAMAGE / DNA-BINDING / GLYCOSIDASE / HYDROLASE / LYASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / ZINC-FINGER / LYASE-DNA COMPLEX / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qi, Y. / Verdine, G.L. | ||||||
![]() | ![]() Title: Strandwise translocation of a DNA glycosylase on undamaged DNA. Authors: Qi, Y. / Nam, K. / Spong, M.C. / Banerjee, A. / Sung, R.J. / Zhang, M. / Karplus, M. / Verdine, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.2 KB | Display | ![]() |
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PDB format | ![]() | 104.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 457.6 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sarC ![]() 3sasC ![]() 3sauC ![]() 3savC ![]() 3sawC ![]() 3sbjC ![]() 2f5oS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 30497.213 Da / Num. of mol.: 1 / Mutation: R112A, Q166C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MUTM / Plasmid: PET24B / Production host: ![]() ![]() References: UniProt: P84131, DNA-(apurinic or apyrimidinic site) lyase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4957.231 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 4900.261 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 157 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 291 K / pH: 7 Details: PEG 8K, SODIUM CACODYLATE, GLYCEROL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 25355 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.406 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2F5O Resolution: 2.15→26.29 Å / SU ML: 2.02 / σ(F): 0.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.47 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→26.29 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 |
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