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Yorodumi- PDB-5mgz: Streptomyces Spheroides NovO (8-demethylnovbiocic acid methyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mgz | ||||||
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Title | Streptomyces Spheroides NovO (8-demethylnovbiocic acid methyltransferase) with SAH | ||||||
Components | 8-demethylnovobiocic acid C(8)-methyltransferase | ||||||
Keywords | TRANSFERASE / C methyltransferase / Novobiocin biosynthesis / SAM dependent | ||||||
Function / homology | Function and homology information 8-demethylnovobiocic acid C8-methyltransferase / 8-demethylnovobiocic acid C8-methyltransferase activity / novobiocin biosynthetic process / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Streptomyces niveus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Chung, C.-W. / Mosley, J. / Sadler, J.C. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Structural and Functional Basis of C-Methylation of Coumarin Scaffolds by NovO. Authors: Sadler, J.C. / Chung, C.H. / Mosley, J.E. / Burley, G.A. / Humphreys, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mgz.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgz.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgz ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgz | 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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Unit cell |
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-Components
#1: Protein | Mass: 26257.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SAH / Source: (gene. exp.) Streptomyces niveus (bacteria) / Gene: novO / Plasmid: PET26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9L9F3, 8-demethylnovobiocic acid C8-methyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 46.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5, 20% w/v poly(ethylene glycol) (PEG)-4K, 0.6 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97916 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80.45 Å / Num. obs: 201009 / % possible obs: 90.7 % / Redundancy: 6 % / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 10.6 / CC1/2: 0.988 / % possible all: 53.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→80.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.21 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.149 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→80.45 Å
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