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Yorodumi- PDB-6j24: Crystal structure of a SAM-dependent methyltransferase LepI in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j24 | ||||||
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Title | Crystal structure of a SAM-dependent methyltransferase LepI in complex with its substrate | ||||||
Components | O-methyltransferase | ||||||
Keywords | TRANSFERASE / Complex | ||||||
Function / homology | Function and homology information : / : / O-methyltransferase activity / secondary metabolite biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation Similarity search - Function | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 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 | 6j24.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j24.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 6j24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j24_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6j24_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6j24_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 6j24_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/6j24 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/6j24 | HTTPS FTP |
-Related structure data
Related structure data | 6j1oSC 6j46C S: Starting model for refinement C: citing same article (ref.) |
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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: 43364.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) / Gene: COH21_002903 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A364MK46, UniProt: B8NJH3*PLUS #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: 2.97 Å3/Da / Density % sol: 58.64 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.10M bis-tris pH 7.0, 35% 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: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.244→47.197 Å / Num. obs: 49185 / % possible obs: 99.33 % / Redundancy: 9.5 % / CC1/2: 0.998 / Net I/σ(I): 19.26 |
Reflection shell | Resolution: 2.244→2.5 Å / Num. unique obs: 10914 / CC1/2: 0.896 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J1O Resolution: 2.244→47.197 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.244→47.197 Å
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Refine LS restraints |
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LS refinement shell |
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