+Open data
-Basic information
Entry | Database: PDB / ID: 7ao5 | ||||||
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Title | Crystal structure of CotB2 variant W288F | ||||||
Components | Cyclooctat-9-en-7-ol synthase | ||||||
Keywords | LYASE / TERPENE SYNTHASE / CYCLOOCTATIN | ||||||
Function / homology | cyclooctat-9-en-7-ol synthase / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / isomerase activity / lyase activity / metal ion binding / Cyclooctat-9-en-7-ol synthase Function and homology information | ||||||
Biological species | Streptomyces melanosporofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Dimos, N. / Driller, R. / Loll, B. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol. Authors: Raz, K. / Driller, R. / Dimos, N. / Ringel, M. / Bruck, T. / Loll, B. / Major, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ao5.cif.gz | 167.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ao5.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ao5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7ao5 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7ao5 | HTTPS FTP |
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-Related structure data
Related structure data | 7ao0C 7ao1C 7ao2C 7ao3C 7ao4C 4omgS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 36731.484 Da / Num. of mol.: 2 / Mutation: W288F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria) Gene: CotB2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/HCl pH 8.5 13.5% (w/v) PEG3350 0.1 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 42357 / % possible obs: 99.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.252 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.06→2.18 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6752 / CC1/2: 0.5 / Rrim(I) all: 1.663 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OMG Resolution: 2.06→47.49 Å / SU ML: 0.2742 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6625 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→47.49 Å
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Refine LS restraints |
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LS refinement shell |
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