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Yorodumi- PDB-2ia6: Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ia6 | ||||||
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Title | Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Benzo pyrene / Carcinogen / Lesion bypass / Polymerase / translesion synthesis / dpo4 / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bauer, J. / Ling, H. / Sayer, J.M. / Xing, G. / Yagi, H. / Jerina, D.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment. Authors: Bauer, J. / Xing, G. / Yagi, H. / Sayer, J.M. / Jerina, D.M. / Ling, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ia6.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ia6.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ia6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/2ia6 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/2ia6 | HTTPS FTP |
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-Related structure data
Related structure data | 2ibkC 1jx4S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40257.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4 / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 4 molecules CEDF
#2: DNA chain | Mass: 4120.695 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 5058.286 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 7 types, 469 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | #10: 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: 2.68 Å3/Da / Density % sol: 54.16 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES, 100 mM calcium acetate, 12% polyethylene glycol 3350, 2% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2004 / Details: Double crystal monochromator |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 37640 / Num. obs: 37640 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3639 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JX4 Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.04
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