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- PDB-4f5o: Open ternary complex of R283K DNA polymerase beta with a one meta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f5o | ||||||
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Title | Open ternary complex of R283K DNA polymerase beta with a one metal bound dCTP analog | ||||||
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![]() | Transferase / Lyase/DNA / Lyase-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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity ...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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / 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 / response to gamma radiation / base-excision repair / spindle microtubule / 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 / microtubule / in utero embryonic development / 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Freudenthal, B.D. / Beard, W.A. / Wilson, S.H. | ||||||
![]() | ![]() Title: Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Authors: Freudenthal, B.D. / Beard, W.A. / Wilson, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799 KB | Display | ![]() |
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Full document | ![]() | 806 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4f5nC ![]() 4f5pC ![]() 4f5qC ![]() 4f5rC ![]() 3isbS 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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Details | The biological assembly is a monomer in each asymetric unit. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38213.656 Da / Num. of mol.: 1 / Mutation: R283K 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: 4860.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 284 molecules ![](data/chem/img/6CF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-6CF / |
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#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50mM Imidazole, 350mM Sodium Acetate, 19% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: May 3, 2011 / Details: Mirrors | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors VarimaxHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→28 Å / Num. all: 151838 / Num. obs: 151838 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 30.93 Å2 / Rmerge(I) obs: 0.056 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ISB Resolution: 2→22.572 Å / SU ML: 0.34 / Isotropic thermal model: Restrained / σ(F): 0 / Phase error: 26.18 / 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: 48.215 Å2 / ksol: 0.365 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2→22.572 Å
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Refine LS restraints |
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LS refinement shell |
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