+Open data
-Basic information
Entry | Database: PDB / ID: 5gut | ||||||||||||
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Title | The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A | ||||||||||||
Components | DNA (cytosine-5)-methyltransferase 1 | ||||||||||||
Keywords | TRANSFERASE / Mutant | ||||||||||||
Function / homology | Function and homology information SUMOylation of DNA methylation proteins / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / PRC2 methylates histones and DNA / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase ...SUMOylation of DNA methylation proteins / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / PRC2 methylates histones and DNA / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / S-adenosylmethionine metabolic process / DNA methylation-dependent heterochromatin formation / female germ cell nucleus / methyl-CpG binding / lncRNA binding / germ cell nucleus / negative regulation of gene expression via chromosomal CpG island methylation / heterochromatin / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / replication fork / methyltransferase activity / promoter-specific chromatin binding / nuclear estrogen receptor binding / cellular response to amino acid stimulus / histone deacetylase binding / regulation of cell population proliferation / methylation / regulation of gene expression / response to xenobiotic stimulus / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||||||||
Authors | Chen, S.J. / Ye, F. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1. Authors: Ye, F. / Kong, X. / Zhang, H. / Liu, Y. / Shao, Z. / Jin, J. / Cai, Y. / Zhang, R. / Li, L. / Zhang, Y.W. / Liu, Y.C. / Zhang, C. / Xie, W. / Yu, K. / Ding, H. / Zhao, K. / Chen, S. / Jiang, ...Authors: Ye, F. / Kong, X. / Zhang, H. / Liu, Y. / Shao, Z. / Jin, J. / Cai, Y. / Zhang, R. / Li, L. / Zhang, Y.W. / Liu, Y.C. / Zhang, C. / Xie, W. / Yu, K. / Ding, H. / Zhao, K. / Chen, S. / Jiang, H. / Baylin, S.B. / Luo, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gut.cif.gz | 194.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gut.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gut_validation.pdf.gz | 728.6 KB | Display | wwPDB validaton report |
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Full document | 5gut_full_validation.pdf.gz | 749.4 KB | Display | |
Data in XML | 5gut_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 5gut_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5gut ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5gut | HTTPS FTP |
-Related structure data
Related structure data | 5guvC 3pt9S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 98850.453 Da / Num. of mol.: 1 / Fragment: UNP residues 731-1602 / Mutation: N1248A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Plasmid: pET28a / Details (production host): His SUMO Tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: 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: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M Tris hydrochloride pH 8.5, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Dec 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→44.36 Å / Num. obs: 57583 / % possible obs: 97 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.1071 / Net I/σ(I): 22.28 |
Reflection shell | Resolution: 2.099→2.174 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PT9 Resolution: 2.099→44.36 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→44.36 Å
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Refine LS restraints |
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LS refinement shell |
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