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Yorodumi- PDB-5eat: 5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM WITH SUBSTRAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eat | ||||||
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Title | 5-EPI-ARISTOLOCHENE SYNTHASE FROM NICOTIANA TABACUM WITH SUBSTRATE ANALOG FARNESYL HYDROXYPHOSPHONATE | ||||||
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 / RIGID BODY REFINEMENT/DIFFERENCE FOURIER MAPS / Resolution: 2.8 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: 1990 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 | 5eat.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eat.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 5eat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/5eat ftp://data.pdbj.org/pub/pdb/validation_reports/ea/5eat | HTTPS FTP |
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-Related structure data
Related structure data | 5easSC 5eauC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 63067.422 Da / Num. of mol.: 1 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q40577 | ||||
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#2: Chemical | #3: Chemical | ChemComp-FHP / | #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: 3.85 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, 2 MM FARNESYL HYDROXYPHOSPHONATE; SOAKING SOLUTION FOR FREEZING ALSO INCLUDED 20% ETHYLENE GLYCOL. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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: Nov 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 24648 / % possible obs: 98.3 % / Observed criterion σ(I): -2 / Redundancy: 5.5 % / Rsym value: 0.152 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.531 / % possible all: 96.3 |
Reflection | *PLUS Num. measured all: 136072 / Rmerge(I) obs: 0.187 |
Reflection shell | *PLUS % possible obs: 96.3 % / Rmerge(I) obs: 0.531 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT/DIFFERENCE FOURIER MAPS Starting model: NATIVE TEAS (PDB ENTRY 5EAS) Resolution: 2.8→100 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 16 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 17 - 24 ARE MODELED, BUT EXHIBIT WEAK DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY ...Details: THE PROTEIN CONSISTS OF RESIDUES 1 - 548. RESIDUES 1 - 16 ARE ABSENT FROM THE ELECTRON DENSITY. RESIDUES 17 - 24 ARE MODELED, BUT EXHIBIT WEAK DENSITY. RESIDUES 97 - 102 EXHIBIT WEAK DENSITY AND MAY BE IN MULTIPLE CONFORMATIONS. RESIDUES 315 - 333 EXHIBIT ANISOTROPIC ELECTRON DENSITY. RESIDUES 522 - 532 WERE DISORDERED IN THE NATIVE STRUCTURE (5EAS) BUT DISPLAY STRONG DENSITY IN THE FARNESYL HYDROXYPHOSPHONATE COMPLEX. RESIDUES 253 - 266 ARE BETTER ORDERED THAN IN THE NATIVE STRUCTURE, AND HAVE TRANSLATED 2-3 ANGSTROMS TOWARD THE ACTIVE SITE.
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Displacement parameters | Biso mean: 28.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.93 Å / Rfactor Rfree error: 0.08 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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