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Yorodumi- PDB-6a5n: Crystal structure of Arabidopsis thaliana SUVH6 in complex with m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a5n | ||||||
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Title | Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA | ||||||
Components |
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Keywords | GENE REGULATION/DNA / SRA / SET / histone methyltransferase / DNA methylation / GENE REGULATION / GENE REGULATION-DNA complex | ||||||
Function / homology | Function and homology information 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 / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Li, X. / Du, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a5n.cif.gz | 248.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a5n.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 6a5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/6a5n ftp://data.pdbj.org/pub/pdb/validation_reports/a5/6a5n | HTTPS FTP |
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-Related structure data
Related structure data | 6a5kSC 6a5mC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Arabidopsis thaliana (thale cress) / Gene: SUVH6, SDG23, SET23, At2g22740, T9I22.18 / Plasmid: pET-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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