[English] 日本語
Yorodumi- PDB-3p5r: Crystal Structure of Taxadiene Synthase from Pacific Yew (Taxus b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p5r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Taxadiene Synthase from Pacific Yew (Taxus brevifolia) in complex with Mg2+ and 2-fluorogeranylgeranyl diphosphate | ||||||
Components | Taxadiene synthase | ||||||
Keywords | LYASE / class I and II terpene cyclase fold / diterpene cyclase / DDXXD motif / NSE/DTE motif / 2-fluoro-geranylgeranyl diphosphate / Biosynthesis of paclitaxel | ||||||
Function / homology | Function and homology information taxadiene synthase / taxadiene synthase activity / paclitaxel biosynthetic process / terpene synthase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Taxus brevifolia (Pacific yew) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 Å | ||||||
Authors | Koksal, M. / Christianson, D.W. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis. Authors: Koksal, M. / Jin, Y. / Coates, R.M. / Croteau, R. / Christianson, D.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3p5r.cif.gz | 336.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3p5r.ent.gz | 267.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/3p5r ftp://data.pdbj.org/pub/pdb/validation_reports/p5/3p5r | HTTPS FTP |
---|
-Related structure data
Related structure data | 3p5pSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 87801.625 Da / Num. of mol.: 2 / Fragment: UNP residues 108-862 Source method: isolated from a genetically manipulated source Details: source tissue: stem, vector: pET22bTV is a derivative of pET22b Source: (gene. exp.) Taxus brevifolia (Pacific yew) / Tissue: stem / Gene: TDC1 / Plasmid: pET22bTV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q41594, taxadiene synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.39 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES (pH 7.0), 20% polyethylene glycol 3350, 200 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.008 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2010 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 70530 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 5.681 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.194 / Num. unique all: 3524 / Rsym value: 0.454 / % possible all: 86.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID: 3P5P Resolution: 2.247→43.409 Å / SU ML: 0.34 / σ(F): 0.08 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.745 Å2 / ksol: 0.348 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.247→43.409 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|