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Open data
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Basic information
Entry | Database: PDB / ID: 5qtj | ||||||
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Title | T. brucei FPPS in complex with CID 47256035 | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | Transferase/Transferase inhibitor / farnesyl diphosphate synthase / Trypanosoma brucei / PanDDA / protein-ligand complex / Transferase-Transferase inhibitor complex | ||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Muenzker, L. / Petrick, J.K. / Schleberger, C. / Cornaciu, I. / Marquez, J.A. / Jahnke, W. | ||||||
![]() | ![]() Title: T. brucei FPPS in complex with CID 47256035 Authors: Muenzker, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.3 KB | Display | ![]() |
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PDB format | ![]() | 120.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002102 (7 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | FPPS screened against the Enamine Golden Fragment Library by X-ray Crystallography at the HTX lab of EMBL Grenoble |
-Related structure data
Related structure data | ![]() 4rypS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42169.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 92 molecules ![](data/chem/img/PJS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PJS / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % / Mosaicity: 0.05 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.12 M CsCl 12 % w/v PEG 3350, 12 % v/v DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.101→57.028 Å / Num. obs: 17890 / % possible obs: 77.9 % / Redundancy: 35.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.021 / Rrim(I) all: 0.128 / Rsym value: 0.134 / Net I/σ(I): 21.7 / Num. measured all: 590391 / Scaling rejects: 2 |
Reflection shell | Resolution: 2.101→2.282 Å / Redundancy: 20.7 % / Rmerge(I) obs: 1.927 / Mean I/σ(I) obs: 1.5 / Num. measured all: 83677 / Num. unique obs: 2286 / CC1/2: 0.952 / Rpim(I) all: 0.247 / Rrim(I) all: 1.504 / Rsym value: 1.927 / Net I/σ(I) obs: 2.7 / % possible all: 18.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 4ryp Resolution: 2.101→57.028 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.76 Å2 / Biso mean: 56.8529 Å2 / Biso min: 17.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.101→57.028 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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