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Yorodumi- PDB-1n48: Y-family DNA polymerase Dpo4 in complex with DNA containing abasi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n48 | ||||||
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Title | Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Y-family / DNA polymerase / DNA lesion bypass / protein-DNA complex / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W. | ||||||
Citation | Journal: To be Published Title: A Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate Authors: Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W. #1: Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Authors: Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n48.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n48.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n48 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n48 | HTTPS FTP |
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-Related structure data
Related structure data | 1jx4S 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 , 2 types, 2 molecules BC
#1: DNA chain | Mass: 4105.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template |
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#2: DNA chain | Mass: 4620.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 40257.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dpo4 / Plasmid: pet22bB / 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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-Non-polymers , 3 types, 393 molecules
#4: Chemical | #5: Chemical | ChemComp-ATP / | #6: 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: 3.13 Å3/Da / Density % sol: 60.66 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG 3350, 0.1 M Hepes, 100 mM calcium acetate, 2.5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 20, 2001 / Details: 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: 2.2→29.4 Å / Num. all: 32093 / Num. obs: 29643 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.239 / % possible all: 60.1 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JX4 Resolution: 2.2→29.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.4 Å
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Refine LS restraints |
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