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- PDB-2ago: Fidelity of Dpo4: effect of metal ions, nucleotide selection and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ago | ||||||
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Title | Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis | ||||||
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![]() | TRANSFERASE/DNA / base stacking / fidelity / metal ion / mismatch / pyrophosphorolysis / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ling, H. / Yang, W. | ||||||
![]() | ![]() Title: Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. Authors: Vaisman, A. / Ling, H. / Woodgate, R. / Yang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
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Full document | ![]() | 471.1 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2agpC ![]() 2agqC ![]() 1jx4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 4425.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
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#2: DNA chain | Mass: 5064.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 39019.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 160 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-POP / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % |
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 29, 2004 |
Radiation | Monochromator: Osmic Focussing Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. all: 13102 / Num. obs: 12652 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JX4 Resolution: 2.85→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 28.564 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.483 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→30 Å
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Xplor file |
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