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- PDB-4qwb: CRYSTAL STRUCTURE of DPO4 LINKER REGION P236A MUTANT WITH AN INCO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qwb | ||||||
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Title | CRYSTAL STRUCTURE of DPO4 LINKER REGION P236A MUTANT WITH AN INCOMING D-dCDP | ||||||
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![]() | TRANSFERASE/DNA / DBH / DPO4 / POLYMERASE / 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 | ![]() ![]() ![]() | ||||||
![]() | Vyas, R. / Suo, Z. | ||||||
![]() | ![]() Title: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Authors: Gaur, V. / Vyas, R. / Fowler, J.D. / Efthimiopoulos, G. / Feng, J.Y. / Suo, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 80.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 846.4 KB | Display | ![]() |
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Full document | ![]() | 848.4 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qw8C ![]() 4qw9C ![]() 4qwaC ![]() 4qwcC ![]() 4qwdC ![]() 4qweC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39193.676 Da / Num. of mol.: 1 / Fragment: Dpo4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3960.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide |
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#3: DNA chain | Mass: 5507.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide |
-Non-polymers , 5 types, 319 molecules ![](data/chem/img/YYY.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-YYY / | ||||||
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#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-ACT / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG 3350, 0.1 M HEPES (PH 7.0), 100MM CALCIUM ACETATE, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 9, 2012 |
Radiation | Monochromator: KOHZU HLD-4 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.82 Å / Num. obs: 49285 / % possible obs: 99.7 % |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 3 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.27 Å
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Refine LS restraints |
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