+Open data
-Basic information
Entry | Database: PDB / ID: 2ps5 | ||||||
---|---|---|---|---|---|---|---|
Title | N225D Trichodiene Synthase: Complex With Mg and Pyrophosphate | ||||||
Components | Trichodiene synthase | ||||||
Keywords | LYASE / Terpenoid synthase fold / site-directed mutagenesis / NSE/DTE motif / magnesium / ethylene glycol | ||||||
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: 2.1 Å | ||||||
Authors | Vedula, L.S. / Cane, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2008 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ps5.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ps5.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 2ps5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ps5_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ps5_full_validation.pdf.gz | 480.5 KB | Display | |
Data in XML | 2ps5_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 2ps5_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/2ps5 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/2ps5 | HTTPS FTP |
-Related structure data
Related structure data | 2ps4C 2ps6C 2ps7C 2ps8C 1jfgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44051.590 Da / Num. of mol.: 2 / Mutation: N225D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: TRI5, TOX 5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13513, trichodiene synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-POP / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.77 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å |
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: 2.1→50 Å / Num. obs: 76255 / % possible obs: 99.7 % / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / Num. unique all: 11062 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1JFG Resolution: 2.1→50 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
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|