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Yorodumi- PDB-1tv9: HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tv9 | ||||||
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Title | HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE | ||||||
Components |
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Keywords | TRANSFERASE/DNA / NUCLEOTIDYLTRANSFERASE / DNA REPAIR / DNA MISMATCH / BASE EXCISION REPAIR / TRANSFERASE-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 / POLB-Dependent Long Patch Base Excision Repair / 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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / 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 / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Krahn, J.M. / Beard, W.M. / Wilson, S.H. | ||||||
Citation | Journal: Structure / Year: 2004 Title: STRUCTURAL INSIGHTS INTO DNA POLYMERASE BETA DETERRENTS FOR MISINCORPORATION SUPPORT OF AN INDUCED-FIT MECHANISM FOR FIDELITY Authors: Krahn, J.M. / Beard, W.M. / Wilson, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tv9.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tv9.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tv9 ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tv9 | HTTPS FTP |
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-Related structure data
Related structure data | 1tvaC 1bpyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 38241.672 Da / Num. of mol.: 1 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 |
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-Non-polymers , 4 types, 790 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % | ||||||||||||||||||||
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Crystal grow | Temperature: 290 K / pH: 7.5 Details: 14% PEG 3350, 350mM sodium Acetate, 50mM imidazole, 10mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.50 | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→52.4 Å / Num. obs: 29484 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.26 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.38 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BPY Resolution: 2→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: PARAMETERS FOR B-FORM SPECIFIC DNA DIHEDRAL RESTRAINTS IN CNS WERE EXCLUDED BECAUSE MANY OF THE NUCLEIC ACIDS DEVIATE FROM STRICT B-FORM GEOMETRY.
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Solvent computation | Solvent model: CNS / Bsol: 75.78 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.028
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Xplor file |
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