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- PDB-8s9m: DNA cytosine-N4 methyltransferase (residues 79-324) from the Bdel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8s9m | |||||||||
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Title | DNA cytosine-N4 methyltransferase (residues 79-324) from the Bdelloid rotifer Adineta vaga | |||||||||
![]() | DNA cytosine-N4 methyltransferase | |||||||||
![]() | TRANSFERASE/INHIBITOR / DNA Cytosine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / TRANSFERASE-INHIBITOR complex | |||||||||
Function / homology | SINEFUNGIN![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhou, J. / Horton, J.R. / Cheng, X. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga. Authors: Zhou, J. / Horton, J.R. / Kaur, G. / Chen, Q. / Li, X. / Mendoza, F. / Wu, T. / Blumenthal, R.M. / Zhang, X. / Cheng, X. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.6 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 695.8 KB | Display | ![]() |
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Full document | ![]() | 697 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s9nC ![]() 8s9oC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 29807.803 Da / Num. of mol.: 1 / Fragment: Methyltransferase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SFG / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.79 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium citrate tribasic monohydrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→41.68 Å / Num. obs: 40906 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 11.81 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.084 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4026 / CC1/2: 0.34 / Rpim(I) all: 0.78 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→41.68 Å
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Refine LS restraints |
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LS refinement shell |
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