+Open data
-Basic information
Entry | Database: PDB / ID: 6ggj | ||||||
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Title | Crystal structure of CotB2 in complex with alendronate | ||||||
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: 2.1 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 | 6ggj.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ggj.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ggj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ggj_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 6ggj_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 6ggj_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 6ggj_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6ggj ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6ggj | HTTPS FTP |
-Related structure data
Related structure data | 6ggiC 6ggkC 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: 36770.523 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-MG / #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: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 26% (v/v) polyethylene glycol 4000, 100 mM Tris at pH 8.5, 150 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2017 |
Radiation | Monochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 33594 / % possible obs: 99.1 % / Redundancy: 3.1 % / Rrim(I) all: 0.14 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2485 / Rrim(I) all: 0.92 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OMG Resolution: 2.1→19.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.83 Å
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Refine LS restraints |
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LS refinement shell |
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