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Yorodumi- PDB-4qeo: crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qeo | ||||||
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Title | crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH | ||||||
Components |
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Keywords | transcription/DNA / SRA / SET / histone methylation / methylated DNA / methylation / transcription-DNA complex | ||||||
Function / homology | Function and homology information methyl-CpNpG binding / methyl-CpNpN binding / peptidyl-lysine methylation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / double-stranded methylated DNA binding / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases ...methyl-CpNpG binding / methyl-CpNpN binding / peptidyl-lysine methylation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / double-stranded methylated DNA binding / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) Synthetic construct (others) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Du, J. / Li, S. / Patel, D.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE. Authors: Du, J. / Johnson, L.M. / Groth, M. / Feng, S. / Hale, C.J. / Li, S. / Vashisht, A.A. / Gallego-Bartolome, J. / Wohlschlegel, J.A. / 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 | 4qeo.cif.gz | 244.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qeo.ent.gz | 190.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qeo_validation.pdf.gz | 806.3 KB | Display | wwPDB validaton report |
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Full document | 4qeo_full_validation.pdf.gz | 820.2 KB | Display | |
Data in XML | 4qeo_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 4qeo_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/4qeo ftp://data.pdbj.org/pub/pdb/validation_reports/qe/4qeo | HTTPS FTP |
-Related structure data
Related structure data | 4qenSC 4qepC 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
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 4598.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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#3: DNA chain | Mass: 4593.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 59686.797 Da / Num. of mol.: 1 / Fragment: functional fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUVH4, KYP, SDG33, SET33, At5g13960, MAC12.7 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: Q8GZB6, histone-lysine N-methyltransferase |
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#4: Protein/peptide | Mass: 1565.797 Da / Num. of mol.: 1 / Fragment: unp residues 2-16 / Source method: obtained synthetically Details: H3(1-15) peptide was synthesized by Tufts University peptide facility. Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133, UniProt: P84233*PLUS |
-Non-polymers , 3 types, 290 molecules
#5: Chemical | ChemComp-SAH / | ||
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#6: Chemical | ChemComp-ZN / #7: 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: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG200, 5% PEG3000, and 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2013 |
Radiation | Monochromator: double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 45325 / Num. obs: 45280 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4469 / Rsym value: 0.769 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4QEN Resolution: 2→41.098 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 22.7 / 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→41.098 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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