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- PDB-4rxd: T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rxd | ||||||
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Title | T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, R. / Liu, Y.-L. / Oldfield, E. | ||||||
![]() | ![]() Title: Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries. Authors: Liu, Y.L. / Cao, R. / Wang, Y. / 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 | ![]() | 234.3 KB | Display | ![]() |
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PDB format | ![]() | 186.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4rxaC ![]() 4rxcC ![]() 4rxeC ![]() 4rypC ![]() 2ogdS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44475.738 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.58 % |
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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: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 28, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 82972 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2OGD Resolution: 2→29.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.137 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.9 Å2 / Biso mean: 28.582 Å2 / Biso min: 10.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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