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- PDB-6b04: Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl dip... -
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Open data
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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) | |||||||||
![]() | Farnesyl diphosphate synthase | |||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / juvenile hormone / farnesyl diphosphate synthase / inhibitor design / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() pheromone biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Picard, M.-E. / Cusson, M. / Shi, R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.2 KB | Display | ![]() |
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PDB format | ![]() | 188.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6b02C ![]() 6b06C ![]() 6b07C ![]() 1yv5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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.) ![]() Plasmid: pET28a / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() 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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