+Open data
-Basic information
Entry | Database: PDB / ID: 8d7f | ||||||
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Title | FlvF from Aspergillus flavus in complex with Bis-Tris | ||||||
Components | Terpene cyclase flvF | ||||||
Keywords | LYASE / fungal protein / terpene cyclase fold / C-N bond formation | ||||||
Function / homology | Lyases; Carbon-oxygen lyases; Acting on phosphates / terpenoid biosynthetic process / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene cyclase flvF Function and homology information | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Tararina, M.A. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2022 Title: Structure of the Repurposed Fungal Terpene Cyclase FlvF Implicated in the C-N Bond-Forming Reaction of Flavunoidine Biosynthesis. Authors: Tararina, M.A. / Yee, D.A. / Tang, Y. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d7f.cif.gz | 547.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d7f.ent.gz | 449 KB | Display | PDB format |
PDBx/mmJSON format | 8d7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/8d7f ftp://data.pdbj.org/pub/pdb/validation_reports/d7/8d7f | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 42538.148 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) (mold) Strain: ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167 Gene: flvF, AFLA_135460 / Plasmid: pET His6 GFP TEV LIC / Details (production host): Addgene #29663 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: B8NHE1, Lyases; Carbon-oxygen lyases; Acting on phosphates #2: Chemical | ChemComp-BTB / #3: Chemical | ChemComp-GOL / 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: 2.54 Å3/Da / Density % sol: 52 % Description: plates approximately 0.1 x 0.1 x 0.01 mm dimension |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM magnesium chloride hexahydrate, 100 mM Bis-Tris pH 6.5, 25% PEG 3350, 10 mM yttrium(III) chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021 |
Radiation | Monochromator: MD2 diffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→97.35 Å / Num. obs: 99760 / % possible obs: 98.9 % / Redundancy: 2 % / Biso Wilson estimate: 39.39 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.032 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.62→2.72 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 9.4 / Num. unique obs: 9657 / CC1/2: 0.474 / Rpim(I) all: 0.096 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold2 model 1c37a Resolution: 2.62→97.35 Å / SU ML: 0.3636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4787 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→97.35 Å
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Refine LS restraints |
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LS refinement shell |
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