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Yorodumi- PDB-2isp: Ternary complex of DNA Polymerase beta with a dideoxy terminated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2isp | ||||||
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Title | Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-methylene triphosphate | ||||||
Components |
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Keywords | TRANSFERASE/DNA / nucleotidyl transferase / DNA polymerase / leaving-group / 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 / 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 / base-excision repair, gap-filling / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / 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 / in utero embryonic development / neuron apoptotic process / response to ethanol / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sucato, C.A. / Upton, T.G. / Kashemirov, B.A. / Martinek, V. / Xiang, Y. / Beard, W.A. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta. Authors: Sucato, C.A. / Upton, T.G. / Kashemirov, B.A. / Batra, V.K. / Martinek, V. / Xiang, Y. / Beard, W.A. / Pedersen, L.C. / Wilson, S.H. / McKenna, C.E. / Florian, J. / Warshel, A. / Goodman, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2isp.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2isp.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 2isp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2isp_validation.pdf.gz | 780.4 KB | Display | wwPDB validaton report |
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Full document | 2isp_full_validation.pdf.gz | 784.9 KB | Display | |
Data in XML | 2isp_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2isp_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isp ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isp | HTTPS FTP |
-Related structure data
Related structure data | 2isoC 2fmpS 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: 4829.133 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3045.005 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: Q3KP48, UniProt: P06746*PLUS, DNA-directed DNA polymerase |
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-Non-polymers , 5 types, 312 molecules
#5: Chemical | ChemComp-MG / | ||||||
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#6: Chemical | #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-GGH / | #9: 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: 2.24 Å3/Da / Density % sol: 45.06 % | ||||||||||||||||||||||||||||||||||||
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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% PEG3350, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 7, 2005 / 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: 2.2→50 Å / Num. all: 21101 / Num. obs: 19344 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2063 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FMP Resolution: 2.2→22.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 154596.44 / 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: 41.1678 Å2 / ksol: 0.323182 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→22.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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