+Open data
-Basic information
Entry | Database: PDB / ID: 5ika | ||||||
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Title | Tobacco 5-epi-aristolochene synthase with PPi | ||||||
Components | 5-epi-aristolochene synthase | ||||||
Keywords | LYASE / terpene synthase / TEAS / diphosphate | ||||||
Function / homology | Function and homology information (+)-2-epi-prezizaene synthase / (-)-alpha-cedrene synthase / 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. / Xu, Y. / Louie, G.V. / Bowman, M. / Noel, J.P. | ||||||
Citation | Journal: J.Antibiot. / Year: 2016 Title: Biosynthetic potential of sesquiterpene synthases: product profiles of Egyptian Henbane premnaspirodiene synthase and related mutants. Authors: Koo, H.J. / Vickery, C.R. / Xu, Y. / Louie, G.V. / O'Maille, P.E. / Bowman, M. / Nartey, C.M. / Burkart, M.D. / 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 | 5ika.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ika.ent.gz | 191.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ika.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ika_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 5ika_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 5ika_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 5ika_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ika ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ika | HTTPS FTP |
-Related structure data
Related structure data | 5ik0C 5ik6C 5ik9C 5ikhC 5im1S 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-DPO / | #4: 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: 3.89 Å3/Da / Density % sol: 68.36 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM MOPSO, pH 7, 200 mM Mg Acetate, 16% PEG 8000 |
-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→50.73 Å / Num. obs: 37117 / % possible obs: 99.94 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07405 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 2.45→2.537 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5174 / Mean I/σ(I) obs: 2.08 / Num. measured obs: 3618 / % possible all: 99.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IM1 Resolution: 2.45→50.73 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→50.73 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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