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Yorodumi- PDB-7o45: Crystal structure of ADD domain of the human DNMT3B methyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o45 | ||||||
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Title | Crystal structure of ADD domain of the human DNMT3B methyltransferase | ||||||
Components | Isoform 6 of DNA (cytosine-5)-methyltransferase 3B | ||||||
Keywords | TRANSFERASE / Methyltransferase 3B / DNA methylation / DNMT3B | ||||||
Function / homology | Function and homology information 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 / Defective pyroptosis / NoRC negatively regulates rRNA expression ...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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Boyko, K.M. / Nikolaeva, A.Y. / Bonchuk, A.N. / Georgiev, P.G. / Popov, V.O. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Structure of the DNMT3B ADD domain suggests the absence of a DNMT3A-like autoinhibitory mechanism. Authors: Boyko, K. / Arkova, O. / Nikolaeva, A. / Popov, V.O. / Georgiev, P. / Bonchuk, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o45.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o45.ent.gz | 169.9 KB | Display | PDB format |
PDBx/mmJSON format | 7o45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o45_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7o45_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7o45_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 7o45_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/7o45 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/7o45 | HTTPS FTP |
-Related structure data
Related structure data | 4qbrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 414 - 554 / Label seq-ID: 6 - 146
NCS ensembles :
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-Components
#1: Protein | Mass: 16556.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli) References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.51 Å3/Da / Density % sol: 51.06 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M NaBr; 0.1M bis-tris-propane pH 7.5; 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 1.284 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.284 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→89.94 Å / Num. obs: 36578 / % possible obs: 92.5 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Net I/σ(I): 10.8 / Num. measured all: 129767 / Scaling rejects: 74 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4qbr Resolution: 2.1→64.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.535 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.67 Å2 / Biso mean: 53.627 Å2 / Biso min: 21.66 Å2
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Refinement step | Cycle: final / Resolution: 2.1→64.38 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / 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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