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Yorodumi- PDB-6a5m: Crystal structure of Arabidopsis thaliana SUVH6 in complex with S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a5m | ||||||
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Title | Crystal structure of Arabidopsis thaliana SUVH6 in complex with SAM, form 2 | ||||||
Components | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6Histone methyltransferase | ||||||
Keywords | GENE REGULATION / SRA / SET / histone methyltransferase / DNA methylation | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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 | 6a5m.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a5m.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 6a5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/6a5m ftp://data.pdbj.org/pub/pdb/validation_reports/a5/6a5m | HTTPS FTP |
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-Related structure data
Related structure data | 6a5kSC 6a5nC 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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Unit cell |
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-Components
#1: Protein | Mass: 59437.230 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: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAM / | #4: 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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M di-Sodium tartrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9777 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 24000 / % possible obs: 98.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1223 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A5K Resolution: 2.301→38.549 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.301→38.549 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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