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Yorodumi- PDB-3c2l: Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch i... -
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-Basic information
Entry | Database: PDB / ID: 3c2l | ||||||
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Title | Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Nucleotidyl Transferase / DNA Polymerase / Misincorporation / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Polymorphism / Sodium / 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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity ...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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Batra, V.K. / Beard, W.A. / Shock, D.D. / Pedersen, L.C. / Wilson, S.H. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Authors: Batra, V.K. / Beard, W.A. / Shock, D.D. / Pedersen, L.C. / 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 | 3c2l.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c2l.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c2l_validation.pdf.gz | 754.1 KB | Display | wwPDB validaton report |
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Full document | 3c2l_full_validation.pdf.gz | 766 KB | Display | |
Data in XML | 3c2l_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 3c2l_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/3c2l ftp://data.pdbj.org/pub/pdb/validation_reports/c2/3c2l | HTTPS FTP |
-Related structure data
Related structure data | 3c2kC 3c2mC 2fmpS S: Starting model for refinement C: citing same article (ref.) |
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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: 3061.004 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, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 4 types, 138 molecules
#5: Chemical | ChemComp-MN / #6: Chemical | #7: Chemical | ChemComp-F2A / | #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: 2.26 Å3/Da / Density % sol: 45.5 % | ||||||||||||
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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, 18% PEG 3350, 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 MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Mar 27, 2007 / 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: 2.6→50 Å / Num. all: 13062 / Num. obs: 13062 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1280 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FMP Resolution: 2.6→23.14 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 442885.45 / 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: 32.1306 Å2 / ksol: 0.30449 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→23.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file |
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