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Yorodumi- PDB-7bzc: Crystal structure of plant sesterterpene synthase AtTPS18 complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bzc | ||||||||||||||||||
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Title | Crystal structure of plant sesterterpene synthase AtTPS18 complexed with farnesyl thiolodiphosphate (FSPP) | ||||||||||||||||||
Components | Terpenoid synthase 18 | ||||||||||||||||||
Keywords | LYASE / terpenoid / terpene synthase / sesterterpene / cyclization mechanism / PLANT PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information sesquiterpene biosynthetic process / Lyases; Carbon-oxygen lyases; Acting on phosphates / cyclase activity / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å | ||||||||||||||||||
Authors | Li, J.X. / Wang, G.D. / Zhang, P. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Plant Commun. / Year: 2020 Title: Molecular Basis for Sesterterpene Diversity Produced by Plant Terpene Synthases. Authors: Chen, Q. / Li, J. / Liu, Z. / Mitsuhashi, T. / Zhang, Y. / Liu, H. / Ma, Y. / He, J. / Shinada, T. / Sato, T. / Wang, Y. / Liu, H. / Abe, I. / Zhang, P. / Wang, G. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bzc.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bzc.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/7bzc ftp://data.pdbj.org/pub/pdb/validation_reports/bz/7bzc | HTTPS FTP |
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-Related structure data
Related structure data | 7bzbC 5eatS 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: 69500.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPS18, At3g14520, MIE1.2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9LUE2, Lyases; Carbon-oxygen lyases; Acting on phosphates | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FPS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% (w/v) PEG 8000, 0.04M potassium phosphate (monobasic), 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→34.445 Å / Num. obs: 38230 / % possible obs: 99.7 % / Redundancy: 10.8 % / CC1/2: 0.998 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.303→2.385 Å / Num. unique obs: 2080 / CC1/2: 0.708 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EAT Resolution: 2.303→34.445 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.6 / Stereochemistry target values: ML
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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 max: 99.95 Å2 / Biso mean: 38.2717 Å2 / Biso min: 14.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.303→34.445 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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