+Open data
-Basic information
Entry | Database: PDB / ID: 5eas | ||||||
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Title | 5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM | ||||||
Components | 5-EPI-ARISTOLOCHENE SYNTHASE | ||||||
Keywords | ISOPRENOID SYNTHASE / ISOPRENOID CYCLASE / 5-EPI-ARISTOLOCHENE SYNTHASE / ISOPRENOID BIOSYNTHESIS / NATURAL PRODUCTS BIOSYNTHESIS | ||||||
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 / MIRAS / Resolution: 2.25 Å | ||||||
Authors | Starks, C.M. / Back, K. / Chappell, J. / Noel, J.P. | ||||||
Citation | Journal: Science / Year: 1997 Title: Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase. Authors: Starks, C.M. / Back, K. / Chappell, J. / Noel, J.P. #1: Journal: Arch.Biochem.Biophys. / Year: 1994 Title: Expression of a Plant Sesquiterpene Cyclase Gene in Escherichia Coli Authors: Back, K. / Yin, S. / Chappell, J. #2: Journal: Plant Physiol. / Year: 1993 Title: Purification and Characterization of an Inducible Sesquiterpene Cyclase from Elicitor-Treated Tobacco Cell Suspension Cultures Authors: Vogeli, U. / Freeman, J.W. / Chappell, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eas.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eas.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5eas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/5eas ftp://data.pdbj.org/pub/pdb/validation_reports/ea/5eas | HTTPS FTP |
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-Related 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: 63067.484 Da / Num. of mol.: 1 / Mutation: EXPRESSED WITH 6-HIS TAG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Strain: NK326 / Cell line: BL21 / Plasmid: PET28B(+) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q40577 | ||
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#2: Chemical | #3: 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: 3.67 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG 8000, 200 MM MG(OAC)2, 100 MM MOPSO PH 6.9, 1MM DTT; SOAKING SOLUTION FOR FREEZING ALSO INCLUDED 20% ETHYLENE GLYCOL. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25 Å / Num. obs: 42946 / % possible obs: 95.2 % / Observed criterion σ(I): -2 / Redundancy: 6.3 % / Rsym value: 0.063 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.275 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 272509 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.275 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.25→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 24 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 24 - 36 ARE MODELED, BUT EXHIBIT WEAK DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK ...Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 24 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 24 - 36 ARE MODELED, BUT EXHIBIT WEAK DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY, AND MAY BE IN MULTIPLE CONFORMATIONS. RESIDUES 253 - 266 EXHIBIT WEAK ELECTRON DENSITY AND MAY BE IN MULTIPLE CONFORMATIONS. RESIDUES 315 - 333 EXHIBIT ANISOTROPIC ELECTRON DENSITY. RESIDUES 522 - 532 ARE ABSENT FROM THE ELECTRON DENSITY.
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Displacement parameters | Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |