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Open data
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Basic information
Entry | Database: PDB / ID: 8sp5 | ||||||
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Title | LINE-1 retrotransposon endonuclease domain complex with Mn2+ | ||||||
![]() | LINE-1 retrotransposon endonuclease | ||||||
![]() | HYDROLASE / LINE-1 retrotransposon / endonuclease / metal ion complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | D'Ordine, A.M. / Jogl, G. / Sedivy, J.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease. Authors: D'Ordine, A.M. / Jogl, G. / Sedivy, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 163.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sp7C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27251.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.14 M ammonium sulfate, 24% polyethylene glycol 5000 monomethyl ether, 5 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→46.55 Å / Num. obs: 25007 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.996 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.23→2.3 Å / Num. unique obs: 2244 / CC1/2: 0.853 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→46.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.28 Å
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Refinement TLS params. | Method: refined / Origin x: 17.9534 Å / Origin y: 16.4569 Å / Origin z: -14.6609 Å
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Refinement TLS group | Selection details: all |