+Open data
-Basic information
Entry | Database: PDB / ID: 5qtc | ||||||
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Title | Unliganded T. brucei FPPS | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE / farnesyl diphosphate synthase / Trypanosoma brucei / PanDDA / protein-ligand 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: 1.645 Å | ||||||
Authors | Muenzker, L. / Petrick, J.P. / Schleberger, C. / Jahnke, W. | ||||||
Citation | Journal: To Be Published Title: Unliganded T. brucei FPPS 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 | 5qtc.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qtc.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 5qtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/5qtc ftp://data.pdbj.org/pub/pdb/validation_reports/qt/5qtc | HTTPS FTP |
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-Group deposition
ID | G_1002101 (1 entries) |
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Title | PanDDA analysis group deposition of ground state model |
Type | ground 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 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.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86C09 |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-DMS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.44 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20 % w/v PEG 3350, 0.2 M sodium tartrate dibasic dihydrate |
-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: Oct 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.645→56.767 Å / Num. obs: 24792 / % possible obs: 54.1 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.127 / Rsym value: 0.092 / Net I/σ(I): 20.3 / Num. measured all: 628869 |
Reflection shell | Resolution: 1.645→1.878 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1.9 / Num. measured all: 92960 / Num. unique obs: 5046 / CC1/2: 0.446 / Rpim(I) all: 2.228 / Rrim(I) all: 9.678 / Rsym value: 1.531 / Net I/σ(I) obs: 0.5 / % possible all: 8.4 |
-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: 1.645→56.767 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.45 / 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: 120.81 Å2 / Biso mean: 44.3119 Å2 / Biso min: 15.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.645→56.767 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 2.6547 Å / Origin y: 11.8524 Å / Origin z: -10.9774 Å
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Refinement TLS group |
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