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Open data
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Basic information
Entry | Database: PDB / ID: 5qt4 | ||||||
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Title | T. brucei FPPS in complex with CID 3599333 | ||||||
![]() | Farnesyl pyrophosphate synthase![]() | ||||||
![]() | TRANSFERASE/TRANSFERASE inhibitor / farnesyl diphosphate synthase / ![]() ![]() | ||||||
Function / homology | ![]() transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Muenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W. | ||||||
![]() | ![]() Title: T. brucei FPPS in complex with CID 3599333 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 | ![]() | 148.2 KB | Display | ![]() |
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PDB format | ![]() | 116.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002098 (8 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | X-ray crystallography of TbruFPPS at Novartis, Basel and data collection at SLS beamline X10SA |
-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
#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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#2: Chemical | ChemComp-P9Y / |
#3: Chemical | ChemComp-PEG / ![]() |
#4: Chemical | ChemComp-DMS / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % / Mosaicity: 0.2 ° |
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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 6M / Detector: PIXEL / Date: Jul 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.324→52.894 Å / Num. obs: 9284 / % possible obs: 52.8 % / Redundancy: 17 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.028 / Rrim(I) all: 0.12 / Rsym value: 0.073 / Net I/σ(I): 26.4 / Num. measured all: 255141 |
Reflection shell | Resolution: 2.324→2.595 Å / Redundancy: 16.4 % / Rmerge(I) obs: 1.862 / Mean I/σ(I) obs: 1.7 / Num. measured all: 42821 / Num. unique obs: 2192 / CC1/2: 0.375 / Rpim(I) all: 3.575 / Rrim(I) all: 16.004 / Rsym value: 1.862 / Net I/σ(I) obs: 0.3 / % possible all: 9.7 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdbid 4ryp Resolution: 2.324→52.894 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.12 / 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: 183.67 Å2 / Biso mean: 80.1337 Å2 / Biso min: 23.55 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.324→52.894 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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