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Yorodumi- PDB-5ily: Tobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ily | ||||||
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Title | Tobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecule and diphosphate (PPi) | ||||||
Components | 5-epi-aristolochene synthase5-epiaristolochene synthase | ||||||
Keywords | LYASE / terpene synthase / TEAS / BIS-TRIS / diphosphate | ||||||
Function / homology | Function and homology information 5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / sesquiterpene biosynthetic process / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Koo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P. | ||||||
Citation | Journal: To Be Published Title: Small-molecule buffer components can directly affect terpene-synthase activity by interacting with the substrate-binding site of the enzyme Authors: Koo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ily.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ily.ent.gz | 193 KB | Display | PDB format |
PDBx/mmJSON format | 5ily.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/5ily ftp://data.pdbj.org/pub/pdb/validation_reports/il/5ily | HTTPS FTP |
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-Related structure data
Related structure data | 5il3C 5il8C 5ildC 5ilhC 5iliC 5iljC 5ilkC 5ilzC 5im1SC C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 63201.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pH9GW / Details (production host): pET28 derived Gateway vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q40577, 5-epiaristolochene synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BTB / | #4: Chemical | ChemComp-DPO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.04 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: Crystallizion reserior:100 mM MOPSO, pH 7, 300 mM Mg Acetate, 13% PEG 8000,Soaked in 50 mM MOPSO (pH 7), 110 mM Mg Acetate, 10% PEG 8000, 10 mM BIS-TRIS (pH 6.5), 1 mM inorganic diphosphate (PPi) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→51.2 Å / Num. obs: 35732 / % possible obs: 94.3 % / Redundancy: 9.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1459 / Net I/σ(I): 10.36 |
Reflection shell | Resolution: 2.45→2.538 Å / Redundancy: 9.8 % / Rmerge(I) obs: 3.322 / Mean I/σ(I) obs: 1.2 / Num. measured obs: 3623 / CC1/2: 0.725 / % possible all: 96.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IM1 Resolution: 2.45→51.198 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54 / 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: 2.45→51.198 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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