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Yorodumi- PDB-8yla: Crystal structures of terpene synthases complexed with a substrat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yla | ||||||
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Title | Crystal structures of terpene synthases complexed with a substrate mimic | ||||||
Components | Sesterfisherol synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / sesterterpene synthase / terpene cyclase / sesterfisherol synthase | ||||||
Function / homology | Function and homology information sesterfisherol synthase / geranylfarnesyl diphosphate synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / terpenoid biosynthetic process / transferase activity / lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Neosartorya fischeri (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Xu, M. / Ma, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024 Title: Structural Insights into the Terpene Cyclization Domains of Two Fungal Sesterterpene Synthases and Enzymatic Engineering for Sesterterpene Diversification. Authors: Ma, M. / Xu, M. / Xu, H. / Lei, Z. / Xing, B. / Dickschat, J.S. / Yang, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yla.cif.gz | 171.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yla.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 8yla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/8yla ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8yla | HTTPS FTP |
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-Related structure data
Related structure data | 8yl9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39208.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / CBS 544.65 / FGSC A1164 / JCM 1740 / NRRL 181 / WB 181) (mold) Gene: NfSS, NFIA_055500 / Production host: Escherichia coli (E. coli) References: UniProt: A1DN30, sesterfisherol synthase, 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.02 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 200 mM Magnesium formate and 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97902 Å |
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: 1.3→30 Å / Num. obs: 149763 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 14701 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→28.65 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.73 / 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: 1.3→28.65 Å
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Refine LS restraints |
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LS refinement shell |
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