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Yorodumi- PDB-9fcq: CysG(N-16)-H122A mutant in complex with SAH from Kitasatospora cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fcq | ||||||
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Title | CysG(N-16)-H122A 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 | Function and homology information | ||||||
Biological species | Kitasatospora cystarginea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 9fcq.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fcq.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 9fcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/9fcq ftp://data.pdbj.org/pub/pdb/validation_reports/fc/9fcq | HTTPS FTP |
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-Related structure data
Related structure data | 9fcdC 9fceC 9fclC 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: 23861.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kitasatospora cystarginea (bacteria) / Gene: cysG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6R556 |
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-Non-polymers , 6 types, 151 molecules
#2: Chemical | ChemComp-SAH / | ||||||
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#3: Chemical | ChemComp-CA / | ||||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-NA / | #7: 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: 2.61 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES; 0.2 M NaCl; 25% PEG 3350 |
-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: Apr 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 50023 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9221 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.148 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057 / 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: 19.866 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→30 Å
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Refine LS restraints |
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