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Yorodumi- PDB-7dmb: Crystal structure of trans-methyltransferase CalH complex with SAH -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dmb | ||||||
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Title | Crystal structure of trans-methyltransferase CalH complex with SAH | ||||||
Components | Putative methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / CalH / Calbistrin A Biosynthesis | ||||||
Function / homology | Methyltransferase type 12 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Putative methyltransferase Function and homology information | ||||||
Biological species | Emericella variicolor (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Tao, H. / Mori, T. / Abe, I. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: One Polyketide Synthase, Two Distinct Products: Trans-Acting Enzyme-Controlled Product Divergence in Calbistrin Biosynthesis. Authors: Tao, H. / Mori, T. / Wei, X. / Matsuda, Y. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dmb.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dmb.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/7dmb ftp://data.pdbj.org/pub/pdb/validation_reports/dm/7dmb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43444.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella variicolor (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A679DLY7 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.0, 20% PEG4000, 0.5 mM SAH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.99 Å / Num. obs: 39461 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.22 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.131 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3199 / CC1/2: 0.717 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→46.99 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.83 / Phase error: 23.3194 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.99 Å
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Refine LS restraints |
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LS refinement shell |
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