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- PDB-3qkj: The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qkj | ||||||
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Title | The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a bis-tris molecule | ||||||
![]() | DNA cytosine-5 methyltransferase 3 beta isoform 6 variant | ||||||
![]() | TRANSFERASE / DNMT3B / PWWP DOMAIN / METHYLTRANSFERASE 3 BETA / SGC / S-ADENOSYL-L-METHIONINE / ZINC-FINGER / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | ![]() DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / methyltransferase activity / Defective pyroptosis ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / methyltransferase activity / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeng, H. / Amaya, M.F. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains. Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.5 KB | Display | ![]() |
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PDB format | ![]() | 183.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.9 KB | Display | ![]() |
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Full document | ![]() | 476.7 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eaeC ![]() 3l42C ![]() 3llrC ![]() 3lyiC ![]() 3mo8C ![]() 3pfsC ![]() 3pmiC ![]() 3qbyC ![]() 3qj6C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16755.896 Da / Num. of mol.: 4 / Fragment: UNP residues 293-442 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BTB / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.93 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6 Details: pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2009 |
Radiation | Monochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 62267 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 51.72 Å2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→34.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.09 Å / Total num. of bins used: 20
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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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