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Yorodumi- PDB-5guc: Crystal structure of CotB2 (apo form) from Streptomyces melanospo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5guc | ||||||
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Title | Crystal structure of CotB2 (apo form) from Streptomyces melanosporofaciens | ||||||
Components | Cyclooctat-9-en-7-ol synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TERPENE CYCLASE FOLD / DITERPENE CYCLASE / LYASE | ||||||
Function / homology | Function and homology information cyclooctat-9-en-7-ol synthase / isomerase activity / lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces melanosporofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Tomita, T. / Kim, S.-Y. / Ozaki, T. / Yoshida, A. / Kuzuyama, T. / Nishiyama, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Structural Insights into the CotB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-en-7-ol Authors: Tomita, T. / Kim, S.-Y. / Teramoto, K. / Meguro, A. / Ozaki, T. / Yoshida, A. / Motoyoshi, Y. / Mori, N. / Ishigami, K. / Watanabe, H. / 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 | 5guc.cif.gz | 255.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5guc.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 5guc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5guc ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5guc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38192.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria) Gene: CotB2 / Plasmid: PHIS8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase #2: Chemical | #3: 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: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M HEPES-NAOH (PH8.0), 1.4M AMMONIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 22, 2009 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.32 Å / Num. obs: 62332 / % possible obs: 99.5 % / Observed criterion σ(I): 2.9 / Redundancy: 7.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.515 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→29.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.812 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.32 Å
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