+Open data
-Basic information
Entry | Database: PDB / ID: 8har | |||||||||
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Title | SAH-bound C-Methyltransferase Fur6 from Streptomyces sp. KO-3988 | |||||||||
Components | Fur6 | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / furaquinocin / biosynthesis | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å | |||||||||
Authors | Noguchi, T. / Nagata, R. / Tomita, T. / Kuzuyama, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: Reductive biosynthesis of meroterpenoids via transient diazotization Authors: Noguchi, T. / Fan, Z. / Moriwaki, Y. / Yamamoto, H. / Nagata, R. / Tomita, T. / Terada, T. / Shimizu, K. / Nishiyama, M. / Kuzuyama, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8har.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8har.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 8har.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8har_validation.pdf.gz | 977.9 KB | Display | wwPDB validaton report |
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Full document | 8har_full_validation.pdf.gz | 979.7 KB | Display | |
Data in XML | 8har_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 8har_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/8har ftp://data.pdbj.org/pub/pdb/validation_reports/ha/8har | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 38448.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: KO-3988 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2L6E4 #2: Chemical | #3: Chemical | ChemComp-TRS / | #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: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG3350, calcium hydroxide, HEPES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→50 Å / Num. obs: 94785 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.984 / Net I/σ(I): 5.93 |
Reflection shell | Resolution: 2.12→2.18 Å / Num. unique obs: 6960 / CC1/2: 0.813 / Rsym value: 0.687 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.12→48.134 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.379 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.188 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→48.134 Å
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Refine LS restraints |
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LS refinement shell |
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