+Open data
-Basic information
Entry | Database: PDB / ID: 2ps7 | ||||||
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Title | Y295F trichodiene synthase | ||||||
Components | Trichodiene synthase | ||||||
Keywords | LYASE / Terpenoid synthase fold / site-directed mutagenesis / 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: 2.35 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ps7.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ps7.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 2ps7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ps7_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 2ps7_full_validation.pdf.gz | 473.1 KB | Display | |
Data in XML | 2ps7_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 2ps7_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/2ps7 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/2ps7 | HTTPS FTP |
-Related structure data
Related structure data | 2ps4C 2ps5C 2ps6C 2ps8C 1jfaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44034.602 Da / Num. of mol.: 2 / Mutation: Y295F 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.89 % |
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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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91756 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91756 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 54251 / Num. obs: 54010 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 3 / Num. unique all: 5349 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1JFA Resolution: 2.35→50 Å / Cross valid method: THROUGHOUT / σ(I): 3 / 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: 56.9 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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