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- PDB-7jk1: Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jk1 | ||||||
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Title | Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion | ||||||
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![]() | TRANSFERASE/DNA / Translesion / DNA synthesis / DNA Replication / DNA damage / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / error-prone translesion synthesis / translesion synthesis / DNA-directed RNA polymerase complex / response to UV ...DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / error-prone translesion synthesis / translesion synthesis / DNA-directed RNA polymerase complex / response to UV / replication fork / manganese ion binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / chromatin binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rechkoblit, O. / Aggarwal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Authors: Rechkoblit, O. / Johnson, R.E. / Gupta, Y.K. / Prakash, L. / Prakash, S. / Aggarwal, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.1 KB | Display | ![]() |
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PDB format | ![]() | 203.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jklC ![]() 7jkpC ![]() 7jl8C ![]() 7jlgC ![]() 5l2xS S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41038.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96LW4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-DNA chain , 2 types, 4 molecules CGDF
#2: DNA chain | Mass: 5078.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3774.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 100 molecules ![](data/chem/img/DCP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 225-250 mM CaCl2 16-19% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→69.95 Å / Num. obs: 27758 / % possible obs: 98.7 % / Redundancy: 2.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.112 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.62→2.74 Å / Rmerge(I) obs: 1.189 / Num. unique obs: 3360 / CC1/2: 0.375 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L2X Resolution: 2.62→39.877 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.35 / 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 max: 213.3 Å2 / Biso mean: 69.95 Å2 / Biso min: 26.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→39.877 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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