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Yorodumi- PDB-5dhk: Nicotiana tabacum 5-epi-aristolochene synthase mutant W273E - alk... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dhk | |||||||||
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Title | Nicotiana tabacum 5-epi-aristolochene synthase mutant W273E - alkylated | |||||||||
Components | 5-epi-aristolochene synthase5-epiaristolochene synthase | |||||||||
Keywords | LYASE / sesquiterpene synthase / 5-epi-aristolochene synthase / farnesylation / active site alkylation | |||||||||
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: 2.43 Å | |||||||||
Model details | alkylated | |||||||||
Authors | Noel, J.P. / Kersten, R.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases. Authors: Kersten, R.D. / Diedrich, J.K. / Yates, J.R. / 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 | 5dhk.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dhk.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 5dhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/5dhk ftp://data.pdbj.org/pub/pdb/validation_reports/dh/5dhk | HTTPS FTP |
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-Related structure data
Related structure data | 5dhiC 5easS 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: 61734.117 Da / Num. of mol.: 1 / Mutation: W273E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pET28 / 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-FAR / | #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: 3.96 Å3/Da / Density % sol: 68.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, MgCl2, MOPSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.12949 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12949 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→50.42 Å / Num. obs: 36829 / % possible obs: 96.88 % / Redundancy: 8.5 % / Net I/σ(I): 32.44 |
Reflection shell | Resolution: 2.43→2.517 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 1.26 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EAS Resolution: 2.43→50.42 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 26.91 / 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: 138.95 Å2 / Biso mean: 53.6436 Å2 / Biso min: 26.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.43→50.42 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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