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- PDB-4qwd: TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qwd | ||||||
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Title | TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)3TC-PPNP | ||||||
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![]() | TRANSFERASE/DNA / Y-FAMILY DNA 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 | ![]() ![]() ![]() | ||||||
![]() | Gaur, V. / 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 | ![]() | 194.6 KB | Display | ![]() |
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PDB format | ![]() | 152.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 839.7 KB | Display | ![]() |
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Full document | ![]() | 851.4 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qw8C ![]() 4qw9C ![]() 4qwaC ![]() 4qwbC ![]() 4qwcC ![]() 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40090.664 Da / Num. of mol.: 1 / Fragment: Dpo4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 3976.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RANDOM SEQUENCE, CHEMICALLY SYNTHESIZED |
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#3: DNA chain | Mass: 4899.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RANDOM SEQUENCE, CHEMICALLY SYNTHESIZED |
-Non-polymers , 3 types, 276 molecules ![](data/chem/img/3TT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-3TT / [[[[( | ||
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#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG 3350 100MM CALCIUM ACETATE 2.5% GLYCEROL 0.1M MES, PH 7.0, 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: Oct 25, 2011 |
Radiation | Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→19.92 Å / Num. obs: 32480 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.5 / % possible all: 94 |
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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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→19.71 Å
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Refine LS restraints |
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