+Open data
-Basic information
Entry | Database: PDB / ID: 9fcl | ||||||
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Title | CysG(N-16) in complex with SAM from Kitasatospora cystarginea | ||||||
Components | SAM-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / Natural Product Biosynthesis / Enzyme Mechanism / Metal Ion interaction / Molecular Docking / Structure Function Relationships | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Kitasatospora cystarginea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 9fcl.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fcl.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 9fcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/9fcl ftp://data.pdbj.org/pub/pdb/validation_reports/fc/9fcl | HTTPS FTP |
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-Related structure data
Related structure data | 9fcdC 9fceC 9fcqC 9fcsC 9fcuC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23928.920 Da / Num. of mol.: 1 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 |
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-Non-polymers , 5 types, 101 molecules
#2: Chemical | ChemComp-SAM / | ||||
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#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
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: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.1 M HEPES, 0.2 M NaCl, 26% PEG 4000 |
-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: 1.75→30 Å / Num. obs: 26735 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.75→1.85 Å / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4054 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.55 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.095 / 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: 31.999 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→30 Å
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Refine LS restraints |
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