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- PDB-1yyu: D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yyu | ||||||
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Title | D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4S)-7-azabisabolene | ||||||
![]() | Trichodiene synthase | ||||||
![]() | LYASE / terpenoid cyclase fold / site-directed mutant / Pyrophosphate / (4S)-7-azabisabolene | ||||||
Function / homology | ![]() trichodiene synthase / sesquiterpenoid biosynthetic process / trichodiene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vedula, L.S. / Rynkiewicz, M.J. / Pyun, H.J. / Coates, R.M. / Cane, D.E. / Christianson, D.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.6 KB | Display | ![]() |
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PDB format | ![]() | 126.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.5 KB | Display | ![]() |
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Full document | ![]() | 520.8 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yj4C ![]() 1yyqC ![]() 1yyrC ![]() 1yysC ![]() 1yytC ![]() 1kizS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Asymmetric unit is biological dimer |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44064.629 Da / Num. of mol.: 2 / Mutation: D100E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 76 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/RAZ.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SAZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/RAZ.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SAZ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-RAZ / ( | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SAZ / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: 2.95→50 Å / Num. obs: 27593 / % possible obs: 97.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 84.9 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3 / Num. unique all: 2697 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KIZ Resolution: 2.95→50 Å / Cross valid method: THROUGHOUT / σ(F): 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: 58 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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