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Yorodumi- PDB-1yys: Y305F Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yys | ||||||
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Title | Y305F Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4S)-7-azabisabolene | ||||||
Components | Trichodiene synthase | ||||||
Keywords | LYASE / terpenoid cyclase fold / site-directed mutant / Pyrophosphate / (4S)-7-azabisabolene | ||||||
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: 2.75 Å | ||||||
Authors | Vedula, L.S. / Rynkiewicz, M.J. / Pyun, H.J. / Coates, R.M. / Cane, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants. Authors: Vedula, L.S. / Rynkiewicz, M.J. / Pyun, H.J. / Coates, R.M. / 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 | 1yys.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yys.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yys_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
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Full document | 1yys_full_validation.pdf.gz | 489.7 KB | Display | |
Data in XML | 1yys_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 1yys_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/1yys ftp://data.pdbj.org/pub/pdb/validation_reports/yy/1yys | HTTPS FTP |
-Related structure data
Related structure data | 1yj4C 1yyqC 1yyrC 1yytC 1yyuC 1jfgS 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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Details | Asymmetric unit is biological dimer |
-Components
#1: Protein | Mass: 44034.602 Da / Num. of mol.: 2 / Mutation: Y305F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: TRI5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13513, trichodiene synthase #2: Chemical | ChemComp-SAZ / ( | #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: 3.67 Å3/Da / Density % sol: 66.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: PEG 8000, SODIUM HEPES, CALCIUM CHLORIDE, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 / Wavelength: 0.9764 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→75 Å / Num. obs: 33388 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3279 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1JFG Resolution: 2.75→75 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues with occupancy zero in entry were refined as alanines.
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Displacement parameters | Biso mean: 67 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→75 Å
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Refine LS restraints |
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