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Yorodumi- PDB-9g0k: CysG(N-16) in complex with SAH (metal free, cocrystallization in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9g0k | ||||||
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Title | CysG(N-16) in complex with SAH (metal free, cocrystallization in presence of EDTA) 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: 2 Å | ||||||
Authors | Kuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: to be published 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 | 9g0k.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9g0k.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 9g0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9g0k_validation.pdf.gz | 952.7 KB | Display | wwPDB validaton report |
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Full document | 9g0k_full_validation.pdf.gz | 955.8 KB | Display | |
Data in XML | 9g0k_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 9g0k_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/9g0k ftp://data.pdbj.org/pub/pdb/validation_reports/g0/9g0k | HTTPS FTP |
-Related structure data
Related structure data | 9fcd |
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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
#1: Protein | Mass: 23928.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kitasatospora cystarginea (bacteria) / Gene: cysG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W6R556 #2: Chemical | #3: Chemical | #4: 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: 54.12 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 0.1 M TRIS, 20% PEG 8000 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 34551 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4670 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.378 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.588 / ESU R Free: 0.174 / 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: 35.743 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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