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Yorodumi- PDB-7w5i: The structure of trichobrasilenol synthase TaTC6 in complex with FPP-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w5i | ||||||
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Title | The structure of trichobrasilenol synthase TaTC6 in complex with FPP-1 | ||||||
Components | Terpene cyclase 6 | ||||||
Keywords | LYASE/METAL BINDING PROTEIN / trichobrasilenol synthase / Trichoderma / sesquiterpene cyclase / farnesyl diphosphate / METAL BINDING PROTEIN / LYASE-METAL BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information (E)-2-epi-beta-caryophyllene synthase / (+)-isoafricanol synthase / pristinol synthase / (-)-beta-caryophyllene synthase / (-)-E-beta-caryophyllene synthase activity / alpha-humulene synthase / alpha-humulene synthase activity / Lyases; Carbon-oxygen lyases; Acting on phosphates / metal ion binding Similarity search - Function | ||||||
Biological species | Trichoderma atroviride (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Chen, C. / Wang, T. / Yang, Y. / Zhang, L. / Ko, T. / Huang, J. / Guo, R. | ||||||
Funding support | China, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Structural insights into the cyclization of unusual brasilane-type sesquiterpenes. Authors: Wang, T. / Yang, Y. / He, M. / Liu, M. / Huang, J.W. / Min, J. / Chen, C.C. / Liu, Y. / Zhang, L. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w5i.cif.gz | 175.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w5i.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 7w5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w5i ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w5i | HTTPS FTP |
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-Related structure data
Related structure data | 7w5fC 7w5gC 7w5hC 7w5jC 4okmS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45690.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoderma atroviride (fungus) / Gene: tatc6 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A5S9I252, Lyases; Carbon-oxygen lyases; Acting on phosphates, alpha-humulene synthase, (E)-2-epi-beta-caryophyllene synthase, (+)-isoafricanol synthase, pristinol synthase, (-)- ...References: UniProt: A0A5S9I252, Lyases; Carbon-oxygen lyases; Acting on phosphates, alpha-humulene synthase, (E)-2-epi-beta-caryophyllene synthase, (+)-isoafricanol synthase, pristinol synthase, (-)-beta-caryophyllene synthase |
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-Non-polymers , 5 types, 770 molecules
#2: Chemical | #3: Chemical | ChemComp-MLI / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: 1.2 M Sodium malonate, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→33.3 Å / Num. obs: 91204 / % possible obs: 98.3 % / Redundancy: 4 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.13→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1664 / CC1/2: 0.92 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4okm Resolution: 2.13→33.3 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.49 Å2 / Biso mean: 20.6887 Å2 / Biso min: 3.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.13→33.3 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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