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- PDB-2ogd: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ogd | ||||||
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Title | T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527 | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX | ||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, R. / Gao, Y. / Robinson, H. / Goddard, A. / Oldfield, E. | ||||||
![]() | ![]() Title: Bisphosphonates: Teaching Old Drugs with New Tricks Authors: Zhang, Y. / Cao, R. / Leon, A. / Guo, R.T. / Krysiak, K. / Yin, F. / Hudock, M.P. / Mukherjee, S. / Gao, Y. / Robinson, H. / Song, Y. / No, J.H. / Hong, W. / Morita, C. / Wang, A.H.-J. / Oldfield, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.6 KB | Display | ![]() |
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PDB format | ![]() | 132.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 51 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2opnC ![]() 2ewgS ![]() 2ogc ![]() 2ogl S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44475.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase |
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-Non-polymers , 6 types, 580 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SUF.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SUF.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 10% MPD, 0.1 AMMONIUM ACETATE, PH 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 123.2 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 61155 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 0.101 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.538 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2EWG Resolution: 2→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72483.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1416 Å2 / ksol: 0.324869 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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