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Open data
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Basic information
Entry | Database: PDB / ID: 1yj4 | ||||||
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Title | Y305F Trichodiene Synthase | ||||||
![]() | Trichodiene synthase | ||||||
![]() | LYASE / terpenoid cyclase fold / site-directed mutant | ||||||
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 | ![]() | 154.9 KB | Display | ![]() |
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PDB format | ![]() | 124.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.3 KB | Display | ![]() |
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Full document | ![]() | 469 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yyqC ![]() 1yyrC ![]() 1yysC ![]() 1yytC ![]() 1yyuC ![]() 1jfaS 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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1 |
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Unit cell |
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Details | The biological assembly is a dimer found in the asymmetric unit. |
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Components
#1: Protein | Mass: 44034.602 Da / Num. of mol.: 2 / Mutation: Y305F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: PEG 8000, Calcium chloride, Sodium HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Nov 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0721 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 54949 / Num. obs: 54949 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.1 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1JFA Resolution: 2.3→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues in PDB that have occupancy zero were refined as alanines.
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Displacement parameters | Biso mean: 54 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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