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Yorodumi- PDB-1jfg: TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jfg | ||||||
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Title | TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WITH DIPHOSPHATE | ||||||
Components | TRICHODIENE SYNTHASE | ||||||
Keywords | LYASE / terpenoid synthase fold | ||||||
Function / homology | Function and homology information trichodiene synthase / sesquiterpenoid biosynthetic process / trichodiene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Fusarium sporotrichioides (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Rynkiewicz, M.J. / Cane, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade. Authors: Rynkiewicz, M.J. / Cane, D.E. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jfg.cif.gz | 163.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfg.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfg ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfg | HTTPS FTP |
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-Related structure data
Related structure data | 1jfaSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44050.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: TRI5 / Plasmid: PZW03 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13513, EC: 4.1.99.6 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-POP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.87 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: PEG 4000, calcium chloride, sodium HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP at 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.01 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 3, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 46785 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.48→2.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.306 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1JFA Resolution: 2.5→14.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. reflection obs: 38849 / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.257 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.335 / Rfactor Rwork: 0.289 |