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- PDB-8yl9: Crystal structures of terpene synthases complexed with a substrat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yl9 | ||||||
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Title | Crystal structures of terpene synthases complexed with a substrate mimic | ||||||
![]() | Sesterbrasiliatriene synthase PbSS | ||||||
![]() | BIOSYNTHETIC PROTEIN / sesterterpene synthase / terpene cyclase / sesterbrasiliatriene synthase | ||||||
Function / homology | ![]() geranylfarnesyl diphosphate synthase / Lyases; Carbon-oxygen lyases; Acting on phosphates / alcohol biosynthetic process / ketone biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / prenyltransferase activity / terpenoid biosynthetic process / lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, M. / Ma, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights Into the Terpene Cyclization Domains of Two Fungal Sesterterpene Synthases and Enzymatic Engineering for Sesterterpene Diversification. Authors: Xu, M. / Xu, H. / Lei, Z. / Xing, B. / Dickschat, J.S. / Yang, D. / Ma, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.7 KB | Display | ![]() |
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PDB format | ![]() | 177.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 57.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ylaC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40323.328 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A2Z6AQX7, Lyases; Carbon-oxygen lyases; Acting on phosphates, geranylgeranyl diphosphate synthase, geranylfarnesyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 200 mM Magnesium formate and 26% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97902 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→44.32 Å / Num. obs: 27686 / % possible obs: 99.6 % / Redundancy: 36.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.75→2.9 Å / Rmerge(I) obs: 0.515 / Num. unique obs: 3987 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→44.32 Å
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Refine LS restraints |
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LS refinement shell |
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