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- PDB-5j0o: Binary complex crystal structure of DNA polymerase Beta with A:A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j0o | ||||||
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Title | Binary complex crystal structure of DNA polymerase Beta with A:A mismatch at the primer terminus | ||||||
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![]() | TRANSFERASE/DNA / DNA Polymerase Beta / mismatch extension / Binary complex / 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batra, V.K. / Wilson, S.H. | ||||||
![]() | ![]() Title: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Authors: Batra, V.K. / Beard, W.A. / Pedersen, L.C. / 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 | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5j0pC ![]() 5j0qC ![]() 5j0rC ![]() 5j0sC ![]() 5j0tC ![]() 5j0uC ![]() 5j0wC ![]() 5j0xC ![]() 5j0yC ![]() 5j29C ![]() 5j2aC ![]() 5j2bC ![]() 5j2cC ![]() 5j2dC ![]() 5j2eC ![]() 5j2fC ![]() 5j2gC ![]() 5j2hC ![]() 5j2iC ![]() 5j2jC ![]() 5j2kC ![]() 5tzvC ![]() 1bpxS 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 / Fragment: UNP residues 7-335 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: 4837.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 421 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: 2.42 Å3/Da / Density % sol: 49.11 % |
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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, 16-18 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Mar 3, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→50 Å / Num. obs: 29993 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Χ2: 0.991 / Net I/av σ(I): 14.223 / Net I/σ(I): 19.8 / Num. measured all: 107384 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BPX Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 45.6844 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 76.15 Å2 / Biso mean: 33.4081 Å2 / Biso min: 11.27 Å2
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Refinement step | Cycle: final / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å
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Xplor file | Serial no: 1 / Param file: AA.param |