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- PDB-3rji: Ternary complex of DNA Polymerase Beta with a gapped DNA containi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rji | ||||||
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Title | Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position paired with non-hydrolyzable dCTP analog (dCMP(CF2)PP) | ||||||
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![]() | Transferase / Lyase/DNA / Mutagenesis / G-T Transversion / DNA Polymerase / oxidative Damage / 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 / 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 | ![]() ![]() | ||||||
![]() | Batra, V.K. / Beard, W.A. / Wilson, S.H. | ||||||
![]() | ![]() Title: Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion Authors: Batra, V.K. / Shock, D.D. / Beard, W.A. / McKenna, C.E. / 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 | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3rjeC ![]() 3rjfC ![]() 3rjgC ![]() 3rjhC ![]() 3rjjC ![]() 3rjkC ![]() 2fmsS 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: 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: 4860.144 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 349 molecules ![](data/chem/img/6CF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-6CF / | ||||||
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#6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, 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: Apr 13, 2006 / Details: Viramax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 24662 / Num. obs: 17014 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.087 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.25 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2FMS Resolution: 2.3→23.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 358581.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4869 Å2 / ksol: 0.322542 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→23.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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