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Open data
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Basic information
Entry | Database: PDB / ID: 6u8x | ||||||
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Title | Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA | ||||||
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![]() | Transferase/DNA / ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() retrotransposon silencing by heterochromatin formation / : / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, L. / Song, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / ...Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / Bashtrykov, P. / Wade, P.A. / Wang, G.G. / Jeltsch, A. / Song, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.7 KB | Display | ![]() |
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PDB format | ![]() | 180.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6u8pC ![]() 6u8vC ![]() 6u8wC ![]() 5yx2S 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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Unit cell |
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Components
-DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ADBC
#1: Protein | Mass: 33186.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9UBC3, ![]() #2: Protein | Mass: 24163.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-DNA chain , 1 types, 2 molecules EF
#3: DNA chain | Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 3 types, 23 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/HOH.gif)
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#4: Chemical | #5: Chemical | ![]() #6: 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: 4.28 Å3/Da / Density % sol: 71.29 % |
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Crystal grow![]() | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 100 mM MgCl2, 7% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.95→42.8826289855 Å / Num. obs: 43984 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 72.2981583492 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.95→3.06 Å / Num. unique obs: 4359 / CC1/2: 0.763 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5YX2 Resolution: 2.95063876297→42.8826289855 Å / SU ML: 0.490640577389 / Cross valid method: FREE R-VALUE / σ(F): 1.9633455681 / Phase error: 28.4198116328 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 92.2683597198 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95063876297→42.8826289855 Å
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Refine LS restraints |
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LS refinement shell |
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