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Open data
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Basic information
Entry | Database: PDB / ID: 5qtk | ||||||
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Title | T. brucei FPPS in complex with CID 69539 | ||||||
![]() | 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. / Cornaciu, I. / Marquez, J.A. / Jahnke, W. | ||||||
![]() | ![]() Title: T. brucei FPPS in complex with CID 69539 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 | ![]() | 152.1 KB | Display | ![]() |
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PDB format | ![]() | 119.8 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
#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-PJP / | ||||
#3: Chemical | ![]() #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.44 % / Mosaicity: 0.06 ° |
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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: Nov 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.857→56.807 Å / Num. obs: 22050 / % possible obs: 67.4 % / Redundancy: 35.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.296 / Rpim(I) all: 0.047 / Rrim(I) all: 0.277 / Rsym value: 0.296 / Net I/σ(I): 14.3 / Num. measured all: 725619 / Scaling rejects: 5 |
Reflection shell | Resolution: 1.857→2.057 Å / Redundancy: 30.9 % / Rmerge(I) obs: 3.265 / Mean I/σ(I) obs: 1.6 / Num. measured all: 104606 / Num. unique obs: 2852 / CC1/2: 0.929 / Rpim(I) all: 0.473 / Rrim(I) all: 2.89 / Rsym value: 3.265 / Net I/σ(I) obs: 2.3 / % possible all: 13.1 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdbid 4ryp Resolution: 1.857→56.807 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.48 / 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: 109.68 Å2 / Biso mean: 38.3209 Å2 / Biso min: 3.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.857→56.807 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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