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Open data
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Basic information
Entry | Database: PDB / ID: 6ipk | ||||||
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Title | Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP | ||||||
![]() | DNA-directed DNA/RNA polymerase mu | ||||||
![]() | TRANSFERASE / DNA Polymerase Mu / DNA break repair / Transferase-dNTP complex / 8-oxo-dGTP | ||||||
Function / homology | ![]() Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, Y.K. / Wu, W.J. / Tsai, M.D. | ||||||
![]() | ![]() Title: Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. Authors: Chang, Y.K. / Huang, Y.P. / Liu, X.X. / Ko, T.P. / Bessho, Y. / Kawano, Y. / Maestre-Reyna, M. / Wu, W.J. / Tsai, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.6 KB | Display | ![]() |
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PDB format | ![]() | 114 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zlcC ![]() 6aecC ![]() 6aehC ![]() 6ak5C ![]() 6ak6C ![]() 6ak8C ![]() 6ak9C ![]() 6akhC ![]() 6ipdC ![]() 6ipeC ![]() 6ipfC ![]() 6ipgC ![]() 6iphC ![]() 6ipiC ![]() 6ipjC ![]() 6iplC ![]() 6ipmC ![]() 6ipnC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40054.434 Da / Num. of mol.: 1 / Mutation: deletions 398-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 104 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/8DG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/8DG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-8DG / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 21351 / % possible obs: 99.9 % / Redundancy: 13.32 % / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.15→2.28 Å / Redundancy: 13.88 % / Mean I/σ(I) obs: 5.78 / Num. unique obs: 3375 / CC1/2: 0.979 / Rrim(I) all: 0.364 / % possible all: 99.8 |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.307 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→30 Å
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Refine LS restraints |
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