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Yorodumi- PDB-3v7k: Co-crystal structure of K72E variant of rat polymerase beta: Enzy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v7k | ||||||
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Title | Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex | ||||||
Components |
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Keywords | Transferase/DNA / Protein-DNA complex / repair polymerase / Transferase-DNA complex | ||||||
Function / homology | Function and homology information Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / salivary gland morphogenesis ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / salivary gland morphogenesis / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / spleen development / 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 / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / DNA replication / 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 / inflammatory response / DNA damage response / apoptotic process / enzyme binding / protein-containing complex / DNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 Å | ||||||
Authors | Rangarajan, S. / Jaeger, J. | ||||||
Citation | Journal: To be Published Title: Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain Authors: Rangarajan, S. / Gridley, C.L. / Firbank, S. / Dalal, S. / Sweasy, J.B. / Jaeger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v7k.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v7k.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 3v7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7k ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39058.371 Da / Num. of mol.: 1 / Mutation: K72E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Polb / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases | ||
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#2: DNA chain | Mass: 2481.652 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: DNA chain | Mass: 3295.203 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.04 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2011 |
Radiation | Monochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.271→30.3 Å / Num. all: 201278 / Num. obs: 23840 / % possible obs: 91.49 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rsym value: 0.062 / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 2.2711→2.3279 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.627 / Rsym value: 0.649 / % possible all: 72.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.271→30.3 Å / SU ML: 0.73 / σ(F): 0.09 / Phase error: 26.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.995 Å2 / ksol: 0.313 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.271→30.3 Å
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Refine LS restraints |
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LS refinement shell |
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