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- PDB-6a5n: Crystal structure of Arabidopsis thaliana SUVH6 in complex with m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a5n | ||||||
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Title | Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA | ||||||
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![]() | GENE REGULATION/DNA / SRA / SET / histone methyltransferase / DNA methylation / GENE REGULATION / GENE REGULATION-DNA complex | ||||||
Function / homology | ![]() methyl-CpNpG binding / methyl-CpNpN binding / [histone H3]-lysine9 N-methyltransferase / histone H3K9me2 methyltransferase activity / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X. / Du, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Authors: Li, X. / Harris, C.J. / Zhong, Z. / Chen, W. / Liu, R. / Jia, B. / Wang, Z. / Li, S. / Jacobsen, S.E. / Du, 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 | ![]() | 248.7 KB | Display | ![]() |
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PDB format | ![]() | 194.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6a5kSC ![]() 6a5mC 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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Unit cell |
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Components
#1: Protein | Mass: 59062.066 Da / Num. of mol.: 1 / Mutation: P777L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8VZ17, histone-lysine N-methyltransferase | ||
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#2: DNA chain | Mass: 4318.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: methylated DNA / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 4255.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: complementary DNA / Source: (synth.) synthetic construct (others) | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% ethanol, 10% w/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 25062 / % possible obs: 97.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2497 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A5K Resolution: 2.4→33.592 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→33.592 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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