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Yorodumi- PDB-6j1o: Crystal structure of a SAM-dependent methyltransferase LepI from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j1o | ||||||
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Title | Crystal structure of a SAM-dependent methyltransferase LepI from Aspergillus flavus | ||||||
Components | O-methyltransferase lepI | ||||||
Keywords | TRANSFERASE / Complex | ||||||
Function / homology | Function and homology information secondary metabolite biosynthetic process / O-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation Similarity search - Function | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Qiu, S. / Wei, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Signal Transduct Target Ther / Year: 2019 Title: Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme. Authors: Sun, Q. / Hu, Y. / Gu, Y. / Huang, J. / He, J. / Luo, L. / Yang, Y. / Yin, S. / Dou, C. / Wang, T. / Fu, X. / He, L. / Qi, S. / Zhu, X. / Yang, S. / Wei, X. / Cheng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j1o.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j1o.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/6j1o ftp://data.pdbj.org/pub/pdb/validation_reports/j1/6j1o | HTTPS FTP |
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-Related 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: 43364.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) (mold) Strain: ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167 Gene: lepI, AFLA_066940 / Production host: Escherichia coli (E. coli) References: UniProt: B8NJH3, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.99 Å3/Da / Density % sol: 58.92 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.15M bis-tris pH 7.0, 40% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jan 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97855 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→53.758 Å / Num. obs: 110825 / % possible obs: 98.06 % / Redundancy: 4.6 % / CC1/2: 0.999 / Net I/σ(I): 23.96 |
Reflection shell | Resolution: 1.7→1.7193 Å / Num. unique obs: 10282 / CC1/2: 0.96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→53.758 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→53.758 Å
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Refine LS restraints |
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LS refinement shell |
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