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- PDB-5db9: Structure of human DNA polymerase beta Host-Guest complex with th... -
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Basic information
Entry | Database: PDB / ID: 5db9 | ||||||
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Title | Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dG | ||||||
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![]() | transferase/dna / human dna polymerase / transferase-dna complex | ||||||
Function / homology | ![]() Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Koag, M.C. / Lee, S. | ||||||
![]() | ![]() Title: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. Authors: Kou, Y. / Koag, M.C. / Lee, 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 | ![]() | 100.6 KB | Display | ![]() |
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PDB format | ![]() | 71.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5db6C ![]() 5db7C ![]() 5db8C ![]() 5dbaC ![]() 5dbbC ![]() 5dbcC C: citing same article ( |
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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: 38241.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 4884.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 3118.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 2 types, 82 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97468 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 16411 / % possible obs: 99.4 % / Redundancy: 4.8 % / Net I/σ(I): 13.8 |
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Processing
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Refinement | Resolution: 2.45→19.82 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 0 / Phase error: 27.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→19.82 Å
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Refine LS restraints |
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LS refinement shell |
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