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Yorodumi- PDB-9fcu: CysG(N-16)-H121A mutant in complex with SAH from Kitasatospora cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fcu | ||||||
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Title | CysG(N-16)-H121A mutant in complex with SAH from Kitasatospora cystarginea | ||||||
Components | SAM-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / Natural Product Biosynthesis / Enzyme Mechanism / Metal Ion interaction / Molecular Docking / Structure Function Relationships | ||||||
Function / homology | : / Methyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / SAM-dependent methyltransferase Function and homology information | ||||||
Biological species | Kitasatospora cystarginea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Deciphering the SAM- and metal-dependent mechanism of O-methyltransferases in cystargolide and belactosin biosynthesis: A structure-activity relationship study. Authors: Kuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fcu.cif.gz | 357.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fcu.ent.gz | 290.4 KB | Display | PDB format |
PDBx/mmJSON format | 9fcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fcu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9fcu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9fcu_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 9fcu_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/9fcu ftp://data.pdbj.org/pub/pdb/validation_reports/fc/9fcu | HTTPS FTP |
-Related structure data
Related structure data | 9fcdC 9fceC 9fclC 9fcqC 9fcsC 9fcxC 9fcyC 9fd3C 9g0kC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 23964.994 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kitasatospora cystarginea (bacteria) / Gene: cysG / Plasmid: pETDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6R556 #2: Chemical | ChemComp-SAH / #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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES; 0.02 M MgCl2; 22% Sodium Polyacrylate 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 85811 / % possible obs: 98.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 12473 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.812 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.328 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→30 Å
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