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- PDB-6b02: Crystal structure of CfFPPS2 (apo form), a lepidopteran type-II f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b02 | ||||||
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Title | Crystal structure of CfFPPS2 (apo form), a lepidopteran type-II farnesyl diphosphate synthase | ||||||
![]() | Farnesyl diphosphate synthase | ||||||
![]() | TRANSFERASE / juvenile hormone / farnesyl diphosphate synthase | ||||||
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 | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 448.9 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b04C ![]() 6b06C ![]() 6b07C ![]() 1yv5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39161.051 Da / Num. of mol.: 2 / 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 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.72 % / Mosaicity: 0.997 ° |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 / Details: 20% PEG4000, 0.1 M sodium acetate |
-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: 2.82→98.45 Å / Num. obs: 23898 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Χ2: 1.138 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.82→98.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.911 / SU B: 26.119 / SU ML: 0.443 / SU R Cruickshank DPI: 1.3114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.311 / ESU R Free: 0.415 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: 212.44 Å2 / Biso mean: 105.202 Å2 / Biso min: 59.92 Å2
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Refinement step | Cycle: final / Resolution: 2.82→98.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.824→2.897 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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