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Yorodumi- PDB-7w5g: The apo structure of trichobrasilenol synthase TaTC6 with the spa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w5g | ||||||
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Title | The apo structure of trichobrasilenol synthase TaTC6 with the space group of orthorhombic | ||||||
Components | Terpene cyclase 6 | ||||||
Keywords | LYASE/METAL BINDING PROTEIN / trichobrasilenol synthase / Trichoderma / sesquiterpene cyclase / farnesyl diphosphate / LYASE / 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 | Hypocrea atroviridis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 7w5g.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w5g.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 7w5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w5g ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w5g | HTTPS FTP |
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-Related structure data
Related structure data | 7w5fC 7w5hC 7w5iC 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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Unit cell |
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-Components
#1: Protein | Mass: 45690.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea atroviridis (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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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.44 % |
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Crystal grow | Temperature: 297 K / Method: evaporation Details: 1.6 M Lithium sulfate, 0.09 M Magnesium sulfate, 50 mM HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97892 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→25 Å / Num. obs: 36792 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.036 / Rrim(I) all: 0.101 / Χ2: 0.698 / Net I/σ(I): 5.7 / Num. measured all: 287793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4okm Resolution: 1.8→23.66 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.08 / 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: 58.58 Å2 / Biso mean: 20.6712 Å2 / Biso min: 4.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→23.66 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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