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- PDB-6sii: T. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sii | |||||||||
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Title | T. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chlorobenzyl)piperidin-4-amine | |||||||||
![]() | Farnesyl pyrophosphate synthase | |||||||||
![]() | TRANSFERASE / sterol biosynthesis / homodimer / farnesyl pyrophosphate synthase / Trypanosoma brucei | |||||||||
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. / Jahnke, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: T. brucei FPPS Authors: Muenzker, L. / Jahnke, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151 KB | Display | ![]() |
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PDB format | ![]() | 119.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 709.1 KB | Display | ![]() |
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Full document | ![]() | 715.8 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 Details: GP is an expression tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-LEZ / ~{ |
#3: Chemical | ChemComp-GOL / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.71 % / Description: needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.12 M CsCl 12 % w/v PEG 3350, 12 % v/v DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.326→57.041 Å / Num. obs: 17624 / % possible obs: 99.4 % / Redundancy: 18.5 % / Biso Wilson estimate: 79.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Rsym value: 0.113 / Net I/σ(I): 15.1 / Num. measured all: 326497 |
Reflection shell | Resolution: 2.326→2.366 Å / Redundancy: 19.6 % / Rmerge(I) obs: 12.631 / Mean I/σ(I) obs: 0.3 / Num. measured all: 48808 / Num. unique obs: 2512 / CC1/2: 0.59 / Rpim(I) all: 1.983 / Rrim(I) all: 8.823 / Rsym value: 12.631 / Net I/σ(I) obs: 0.4 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | Model details: Phaser MODE: MR_TRA
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 4ryp Resolution: 2.33→57.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.261
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Displacement parameters | Biso max: 228.35 Å2 / Biso mean: 121.49 Å2 / Biso min: 64.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→57.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 41
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Refinement TLS params. | Method: refined / Origin x: 3.4606 Å / Origin y: 11.916 Å / Origin z: -11.451 Å
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Refinement TLS group | Selection details: { A|* } |