+Open data
-Basic information
Entry | Database: PDB / ID: 5qt4 | ||||||
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Title | T. brucei FPPS in complex with CID 3599333 | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / farnesyl diphosphate synthase / Trypanosoma brucei / PanDDA / protein-ligand complex / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | Function and homology information transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.324 Å | ||||||
Authors | Muenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W. | ||||||
Citation | Journal: To Be Published Title: T. brucei FPPS in complex with CID 3599333 Authors: Muenzker, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qt4.cif.gz | 148.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qt4.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 5qt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/5qt4 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/5qt4 | 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 |
-Links
-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.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86C09 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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