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- PDB-4c8k: Crystal structure of the large fragment of DNA polymerase I from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c8k | |||||||||
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Title | Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP | |||||||||
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![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / UNNATURAL NUCLEOTIDE / ARTIFICIAL NUCLEOTIDE / BINARY COMPLEX / KLENTAQ | |||||||||
Function / homology | ![]() nucleoside binding / 5'-3' exonuclease activity / 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 | ![]() | 363.7 KB | Display | ![]() |
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PDB format | ![]() | 297.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4c8lC ![]() 4c8mC ![]() 4c8nC ![]() 4c8oC ![]() 4cchC ![]() 3m8sS ![]() 4c8j C: citing same article ( S: Starting model for refinement |
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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: 60936.965 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832 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: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PRIMER' / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 4964.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 150 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/BMR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BMR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-BMR / (( | #6: Chemical | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | 5'-AA 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: 2.54 Å3/Da / Density % sol: 51.58 % / Description: NONE |
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Crystal grow | pH: 7 Details: 15% W/V PEG 8000, 100MM TRIS PH 7.0, 200MM MAGNESIUM FORMIAT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2012 / 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: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→48.6 Å / Num. obs: 34375 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 42.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 2.16→2.29 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.47 / CC1/2: 0.478 / % possible all: 51.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3m8s Resolution: 2.17→48.637 Å / SU ML: 0.25 / σ(F): 16.32 / Phase error: 26.44 / Stereochemistry target values: ML / Details: RESIDUES 643-660 HAVE HIGH B- -FACTORS
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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: 51.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→48.637 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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