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Yorodumi- PDB-6v0k: Crystal structure of Penicillium verruculosum copalyl diphosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v0k | ||||||
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Title | Crystal structure of Penicillium verruculosum copalyl diphosphate synthase (PvCPS) alpha prenyltransferase domain | ||||||
Components | Terpene synthase | ||||||
Keywords | TRANSFERASE / Isoprenoid synthase / prenyltransferase | ||||||
Function / homology | Function and homology information copalyl diphosphate synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / isoprenoid biosynthetic process / isomerase activity / transferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Talaromyces verruculosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Christianson, D.W. / Ronnebaum, T.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Higher-order oligomerization of a chimeric alpha beta gamma bifunctional diterpene synthase with prenyltransferase and class II cyclase activities is concentration-dependent. Authors: Ronnebaum, T.A. / Gupta, K. / 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 | 6v0k.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v0k.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 6v0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/6v0k ftp://data.pdbj.org/pub/pdb/validation_reports/v0/6v0k | HTTPS FTP |
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-Related structure data
Related structure data | 2q80S S: Starting model for refinement |
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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: 34787.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces verruculosus (fungus) / Gene: PvCPS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A348FUE1 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.21 Å3/Da / Density % sol: 70.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 7.5 mg/mL PvCPS, 0.1 M sodium citrate tribasic pH 5.7, 2% Tacsimate pH 5.0, 19% PEG-3350. (1:1) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→81.46 Å / Num. obs: 44302 / % possible obs: 99.78 % / Redundancy: 2 % / Biso Wilson estimate: 25.34 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.09308 / Rpim(I) all: 0.09308 / Net I/σ(I): 7.01 |
Reflection shell | Resolution: 2.41→2.496 Å / Rmerge(I) obs: 0.3406 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 4386 / CC1/2: 0.496 / Rpim(I) all: 0.3406 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q80 Resolution: 2.41→81.46 Å / SU ML: 0.3042 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→81.46 Å
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Refine LS restraints |
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LS refinement shell |
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