+Open data
-Basic information
Entry | Database: PDB / ID: 6ggk | ||||||
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Title | Crystal structure of CotB2 C-terminal truncation | ||||||
Components | Cyclooctat-9-en-7-ol synthase | ||||||
Keywords | LYASE / terpene synthase / cyclooctatin | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Driller, R. / Janke, S. / Fuchs, M. / Warner, E. / Mhashal, A.R. / Major, D.T. / Christmann, M. / Brueck, T. / Loll, B. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis. Authors: Driller, R. / Janke, S. / Fuchs, M. / Warner, E. / Mhashal, A.R. / Major, D.T. / Christmann, M. / Bruck, T. / Loll, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ggk.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ggk.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ggk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ggk_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 6ggk_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 6ggk_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 6ggk_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6ggk ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6ggk | HTTPS FTP |
-Related structure data
Related structure data | 6ggiC 6ggjC 6gglC 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: 33837.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria) Gene: CotB2 / Production host: Escherichia coli (E. coli) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 16% (v/v) polyethylene glycol 4000, 100 mM Tris at pH 8.5, 100 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 36510 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rrim(I) all: 0.333 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5766 / Rrim(I) all: 2.087 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OMG Resolution: 2.15→49.857 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→49.857 Å
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Refine LS restraints |
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LS refinement shell |
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