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Yorodumi- PDB-1khc: Crystal Structure of the PWWP Domain of Mammalian DNA Methyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1khc | ||||||
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Title | Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b | ||||||
Components | DNA cytosine-5 methyltransferase 3B2 | ||||||
Keywords | TRANSFERASE / Five beta-sheets barrel followed by Five-helix bundle | ||||||
Function / homology | Function and homology information : / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / : / heterochromatin => GO:0000792 / : / SUMOylation of DNA methylation proteins / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / PRC2 methylates histones and DNA / epigenetic programming of gene expression ...: / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / : / heterochromatin => GO:0000792 / : / SUMOylation of DNA methylation proteins / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / PRC2 methylates histones and DNA / epigenetic programming of gene expression / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-containing complex localization / : / negative regulation of gene expression, epigenetic / : / chromosome, centromeric region / heterochromatin / positive regulation of neuron differentiation / methyltransferase activity / cellular response to amino acid stimulus / histone deacetylase binding / transcription corepressor activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.8 Å | ||||||
Authors | Qiu, C. / Sawada, K. / Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Authors: Qiu, C. / Sawada, K. / Zhang, X. / Cheng, X. | ||||||
History |
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Remark 600 | HETEROGEN THE AUTHORS WERE UNABLE TO FIGURE OUT THE IDENTITY OF THE MOLECULES LABELED AS "UNX" FROM ...HETEROGEN THE AUTHORS WERE UNABLE TO FIGURE OUT THE IDENTITY OF THE MOLECULES LABELED AS "UNX" FROM THE ELECTRON DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1khc.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1khc.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 1khc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1khc ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1khc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16670.039 Da / Num. of mol.: 1 / Fragment: PWWP domain (residues 219-365) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt3b / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O88509, DNA (cytosine-5-)-methyltransferase | ||
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#2: Chemical | ChemComp-UNX / #3: 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: 2.25 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 8000, 0.1M sodium cacodylate, 0.2M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å | |||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 2000 | |||||||||
Radiation | Monochromator: confocal multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 1.8→20 Å / Num. all: 15308 / Num. obs: 15308 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.6 | |||||||||
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 9.4 / % possible all: 94.3 | |||||||||
Reflection | *PLUS Num. measured all: 145433 | |||||||||
Reflection shell | *PLUS % possible obs: 94.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 15.442 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.282 / % reflection Rfree: 11.4 % / Rfactor Rwork: 0.275 |