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- PDB-8k76: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k76 | ||||||
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Title | Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum | ||||||
![]() | S-adenosylmethionine-dependent methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase | ||||||
Function / homology | Methyltransferase type 11 / Methyltransferase domain / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | He, S.R. / Bai, X. / Zhang, J. / Zhao, Z.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum Authors: He, S.R. / Bai, 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 | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 446.7 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28612.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: FN1919 / Production host: ![]() ![]() References: UniProt: Q8R6D8, Transferases; Transferring one-carbon groups; Methyltransferases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3350,sodium citrate, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.489→33 Å / Num. obs: 1036260 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.49→1.52 Å / Num. unique obs: 42568 / CC1/2: 0.999 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→33 Å
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Refine LS restraints |
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LS refinement shell |
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