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- PDB-8te3: Crystal structure of the methyltransferase domain of R882C/R676K ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8te3 | ||||||
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Title | Crystal structure of the methyltransferase domain of R882C/R676K DNMT3A homotetramer | ||||||
![]() | DNA (cytosine-5)-methyltransferase 3A![]() | ||||||
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Function / homology | ![]() positive regulation of cellular response to hypoxia / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, J.W. / Song, J.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the homo-tetrameric DNMT3A methyltransferase domain(R882C/R676K) Authors: Lu, J.W. / Song, J.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 | ![]() | 360.9 KB | Display | ![]() |
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PDB format | ![]() | 289.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yx2S S: Starting model for refinement |
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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: 32777.773 Da / Num. of mol.: 8 / Fragment: methyltransferase domain (UNP residues 628-912) / Mutation: R882C,R676K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9Y6K1, ![]() ![]() #2: Chemical | ChemComp-SAH / ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.9 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2-0.4 M potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 64344 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.07 Å2 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.161 / Rrim(I) all: 0.334 / Χ2: 0.674 / Net I/σ(I): 2.5 / Num. measured all: 273938 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 5YX2 Resolution: 3.2→46.96 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.67 Å2 / Biso mean: 56.5082 Å2 / Biso min: 17.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→46.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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