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Yorodumi- PDB-3q0c: Crystal structure of SUVH5 SRA-fully methylated CG DNA complex in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q0c | ||||||
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Title | Crystal structure of SUVH5 SRA-fully methylated CG DNA complex in space group P6122 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / SRA / fully methylated CG / SUVH5 / 5mC binding protein / Fully methylated CG DNA Duplex / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information regulatory ncRNA-mediated heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / histone H3K9me2 methyltransferase activity / histone methyltransferase activity / chromosome, centromeric region / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / double-stranded DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6567 Å | ||||||
Authors | Eerappa, R. / Simanshu, D.K. / Patel, D.J. | ||||||
Citation | Journal: Genes Dev. / Year: 2011 Title: A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Authors: Rajakumara, E. / Law, J.A. / Simanshu, D.K. / Voigt, P. / Johnson, L.M. / Reinberg, D. / Patel, D.J. / Jacobsen, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q0c.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q0c.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 3q0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q0c_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 3q0c_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 3q0c_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3q0c_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/3q0c ftp://data.pdbj.org/pub/pdb/validation_reports/q0/3q0c | HTTPS FTP |
-Related structure data
Related structure data | 3q0bSC 3q0dC 3q0fC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 18515.920 Da / Num. of mol.: 2 / Fragment: SUVH5 SRA Domain (UNP Residues 362-528) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g35160, SDG9, SET9, SUVH5, T4C15.17 / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: O82175, histone-lysine N-methyltransferase #2: DNA chain | Mass: 3362.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically Synthesized #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 23% PEG 3350, 100 mM Bis-Trispropane, pH 7.0, 80 mM Mg-acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 17149 / Num. obs: 17149 / % possible obs: 100 % / Redundancy: 28.1 % / Rmerge(I) obs: 0.136 / Rsym value: 0.134 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 28.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3 / Rsym value: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q0B Resolution: 2.6567→19.847 Å / SU ML: 0.98 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.92 / 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 / Bsol: 34.098 Å2 / ksol: 0.276 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6567→19.847 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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