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Open data
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Basic information
Entry | Database: PDB / ID: 2ps4 | ||||||
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Title | N225D trichodiene synthase | ||||||
![]() | Trichodiene synthase | ||||||
![]() | LYASE / Terpenoid synthase fold / site-directed mutagenesis / NSE/DTE motif / magnesium / ethylene glycol | ||||||
Function / homology | ![]() trichodiene synthase / sesquiterpenoid biosynthetic process / trichodiene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vedula, L.S. / Cane, D.E. / Christianson, D.W. | ||||||
![]() | ![]() Title: Structural and mechanistic analysis of trichodiene synthase using site-directed mutagenesis: probing the catalytic function of tyrosine-295 and the asparagine-225/serine-229/glutamate-233-Mg2+B motif. Authors: Vedula, L.S. / Jiang, J. / Zakharian, T. / Cane, D.E. / Christianson, D.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.4 KB | Display | ![]() |
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PDB format | ![]() | 123.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
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Full document | ![]() | 473.9 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ps5C ![]() 2ps6C ![]() 2ps7C ![]() 2ps8C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 44051.590 Da / Num. of mol.: 2 / Mutation: N225D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.49 % |
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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 315 / Detector: CCD / Date: Nov 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→87.37 Å / Num. obs: 46906 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 64.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.46→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2 / Num. unique all: 6927 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JFA Resolution: 2.46→87.37 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues with side chain B-factors = 20.00 were refined as alanines due to disorder
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Displacement parameters | Biso mean: 60 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.46→87.37 Å
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Refine LS restraints |
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