+Open data
-Basic information
Entry | Database: PDB / ID: 1kiy | ||||||
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Title | D100E trichodiene synthase | ||||||
Components | trichodiene synthase | ||||||
Keywords | LYASE / terpenoid synthase fold / site-directed mutant | ||||||
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: 2.4 Å | ||||||
Authors | Rynkiewicz, M.J. / Cane, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: X-ray crystal structures of D100E trichodiene synthase and its pyrophosphate complex reveal the basis for terpene product diversity. Authors: Rynkiewicz, M.J. / 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 | 1kiy.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kiy.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kiy_validation.pdf.gz | 389.2 KB | Display | wwPDB validaton report |
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Full document | 1kiy_full_validation.pdf.gz | 400.3 KB | Display | |
Data in XML | 1kiy_validation.xml.gz | 16 KB | Display | |
Data in CIF | 1kiy_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/1kiy ftp://data.pdbj.org/pub/pdb/validation_reports/ki/1kiy | HTTPS FTP |
-Related structure data
Related structure data | 1kizC 1jfgS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The biological dimer can be generated by applying transformation 6_665 to chain A and 6_655 to chain B |
-Components
#1: Protein | Mass: 44064.629 Da / Num. of mol.: 2 / Mutation: D100E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: Tri5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13513, EC: 4.1.99.6 #2: Chemical | ChemComp-EDO / #3: 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: 3.73 Å3/Da / Density % sol: 67.05 % | |||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Rynkiewicz, M.J., (2001) Proc.Natl.Acad.Sci.U.S.J., 98, 13543. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 14, 2001 |
Radiation | Monochromator: SI-111 + SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. all: 52327 / Num. obs: 52222 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 27.4 Å2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.3 % / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 295631 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.366 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1JFG Resolution: 2.4→24.57 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 383948.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.3583 Å2 / ksol: 0.327032 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.215 / Rfactor Rfree: 0.248 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.334 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.28 |