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- PDB-4e1e: Crystal structure of Trypanosome cruzi farnesyl diphosphate synth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4e1e | ||||||
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Title | Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-hexylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+ | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / geranyl transferase / farnesyl pyrophosphate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aripirala, S. / Amzel, L.M. / Gabelli, S.B. | ||||||
![]() | ![]() Title: Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase. Authors: Aripirala, S. / Szajnman, S.H. / Jakoncic, J. / Rodriguez, J.B. / Docampo, R. / Gabelli, S.B. / Amzel, L.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 | ![]() | 87.5 KB | Display | ![]() |
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PDB format | ![]() | 64.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4dwbC ![]() 4dwgSC ![]() 4dxjC ![]() 4dzwC 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41094.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q95WL3, (2E,6E)-farnesyl diphosphate synthase |
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-Non-polymers , 5 types, 29 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/0MW.gif)
![](data/chem/img/IPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0MW.gif)
![](data/chem/img/IPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-0MW / [ | #4: Chemical | ChemComp-IPE / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→65.656 Å / Num. obs: 12287 / % possible obs: 95.7 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.105 / Χ2: 2.266 / Net I/σ(I): 12.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4DWG Resolution: 2.65→28.969 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.838 / WRfactor Rfree: 0.3 / WRfactor Rwork: 0.2219 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7924 / SU B: 15.014 / SU ML: 0.315 / SU Rfree: 0.4277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.94 Å2 / Biso mean: 51.3117 Å2 / Biso min: 16.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→28.969 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.792 Å / Total num. of bins used: 10
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