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- PDB-4c8o: Binary complex of the large fragment of DNA polymerase I from The... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c8o | |||||||||
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Title | Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 2) | |||||||||
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![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA POLYMERASE / UNNATURAL BASE PAIR / ARTIFICIAL BASE PAIR / BINARY COMPLEX / KLENTAQ | |||||||||
Function / homology | ![]() nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Romesberg, F.E. / Marx, A. | |||||||||
![]() | ![]() Title: Structural Insights Into DNA Replication without Hydrogen Bonds. Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Romesberg, F.E. / Marx, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 364.2 KB | Display | ![]() |
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PDB format | ![]() | 299.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.7 KB | Display | ![]() |
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Full document | ![]() | 474.8 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c8kC ![]() 4c8lC ![]() 4c8mC ![]() 4c8nC ![]() 4cchC ![]() 4c8j 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: 60936.965 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832 Source method: isolated from a genetically manipulated source Details: OPEN CONFORMATION OF ENZYME TRAPPED BY CRYSTAL CONTACTS Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3384.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 4295.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 246 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | 5'-TT OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.53 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 30% W/V PEG 5000MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2013 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.2 Å / Num. obs: 66214 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 35.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.73 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.99 / CC1/2: 0.527 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.75→47.876 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 29.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.876 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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