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Yorodumi- PDB-6b04: Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl dip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b04 | |||||||||
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Title | Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid (inhibitor 1b) | |||||||||
Components | Farnesyl diphosphate synthase | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / juvenile hormone / farnesyl diphosphate synthase / inhibitor design / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information pheromone biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Choristoneura fumiferana (eastern spruce budworm) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | |||||||||
Authors | Picard, M.-E. / Cusson, M. / Shi, R. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Insect Biochem. Mol. Biol. / Year: 2017 Title: Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design. Authors: Picard, M.E. / Nisole, A. / Beliveau, C. / Sen, S. / Barbar, A. / Shi, R. / Cusson, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b04.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b04.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 6b04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/6b04 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b04 | HTTPS FTP |
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-Related structure data
Related structure data | 6b02C 6b06C 6b07C 1yv5S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39161.051 Da / Num. of mol.: 3 / Fragment: UNP residues 57-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Choristoneura fumiferana (eastern spruce budworm) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3) References: UniProt: Q1XAB1, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: 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: 3.22 Å3/Da / Density % sol: 61.78 % / Mosaicity: 0.572 ° |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 20% PEG3350, 0.2 M ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 20, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.82→101.18 Å / Num. obs: 131301 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Χ2: 1.019 / Net I/σ(I): 12.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YV5 Resolution: 1.83→101.18 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.382 / SU ML: 0.071 / SU R Cruickshank DPI: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.61 Å2 / Biso mean: 33.66 Å2 / Biso min: 13.03 Å2
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Refinement step | Cycle: final / Resolution: 1.83→101.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.825→1.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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