[English] 日本語
Yorodumi- PDB-4o5e: Structure of human DNA polymerase complexed with N7MG in the temp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o5e | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human DNA polymerase complexed with N7MG in the template base paired with incoming non-hydrolyzable TTP | ||||||
Components |
| ||||||
Keywords | Transferase / Lyase/DNA / DNA binding / polymerase fold / nucleotidyl transfer / DNA / nucleus / Lyase-DNA complex | ||||||
Function / homology | Function and homology information 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 / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / POLB-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 / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.532 Å | ||||||
Authors | Koag, M.C. / Lee, S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine. Authors: Koag, M.C. / Kou, Y. / Ouzon-Shubeita, H. / Lee, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4o5e.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4o5e.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 4o5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/4o5e ftp://data.pdbj.org/pub/pdb/validation_reports/o5/4o5e | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37536.770 Da / Num. of mol.: 1 / Fragment: DNA polymerase beta Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli) References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
---|
-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 4877.169 Da / Num. of mol.: 1 / Fragment: template DNA / Source method: obtained synthetically / Details: synthetic template DNA / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 3085.029 Da / Num. of mol.: 1 / Fragment: up primer DNA / Source method: obtained synthetically / Details: synthetic up primer / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Fragment: down primer DNA / Source method: obtained synthetically / Details: synthetic down primer / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 75 molecules
#5: Chemical | ChemComp-MG / | ||||
---|---|---|---|---|---|
#6: Chemical | #7: Chemical | ChemComp-1FZ / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: 14%-23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å |
---|---|
Detector | Detector: AREA DETECTOR / Date: Oct 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 2.532→20 Å / Num. all: 14851 / Num. obs: 14806 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.532→19.73 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 0 / Phase error: 29.25 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.67 Å2 / Biso mean: 34.6507 Å2 / Biso min: 11.79 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.532→19.73 Å
|