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Open data
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Basic information
Entry | Database: PDB / ID: 8h72 | ||||||
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Title | Class I sesquiterpene synthase DbPROS (complex) | ||||||
![]() | Delta(6)-protoilludene synthase K435DRAFT_659367 | ||||||
![]() | STRUCTURAL PROTEIN / class I sesquiterpene synthase DbPROS (complex) | ||||||
Function / homology | Delta6-protoilludene synthase / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / N-benzyl-N,N-diethylethanaminium / Delta(6)-protoilludene synthase K435DRAFT_659367![]() | ||||||
Biological species | Dendrothele bispora | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lou, T.T. / Ma, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis. Authors: Lou, T. / Li, A. / Xu, H. / Pan, J. / Xing, B. / Wu, R. / Dickschat, J.S. / Yang, D. / Ma, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.3 KB | Display | ![]() |
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PDB format | ![]() | 121.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h4pC ![]() 8h6qC ![]() 8h6uC 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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Unit cell |
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Components
#1: Protein | Mass: 41437.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: K435DRAFT_659367 / Production host: ![]() ![]() References: UniProt: A0A4S8MAF3, Delta6-protoilludene synthase #2: Chemical | #3: Chemical | #4: 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: 2.14 Å3/Da / Density % sol: 42.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 23% w/v PEG 3350, 0.1 M Bistris propane, 200 mM Sodium fluoride, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→53.56 Å / Num. obs: 43108 / % possible obs: 99.4 % / Redundancy: 11 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.09→2.15 Å / Rmerge(I) obs: 0.475 / Num. unique obs: 3154 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Alphafold 2 prediction Resolution: 2.09→53.56 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.74 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→53.56 Å
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Refine LS restraints |
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LS refinement shell |
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