+Open data
-Basic information
Entry | Database: PDB / ID: 5qtd | ||||||
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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: 1.642 Å | ||||||
Authors | Muenzker, L. / Petrick, J.K. / Schleberger, C. / Cornaciu, I. / Marquez, J.A. / 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 | 5qtd.cif.gz | 149.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qtd.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 5qtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/5qtd ftp://data.pdbj.org/pub/pdb/validation_reports/qt/5qtd | HTTPS FTP |
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-Group deposition
ID | G_1002103 (1 entries) |
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Title | PanDDA analysis group deposition of ground-state model |
Type | ground 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 |
-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 | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-GOL / | #5: 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: 2.13 Å3/Da / Density % sol: 42.17 % / Mosaicity: 0.09 ° |
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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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.642→56.678 Å / Num. obs: 27755 / % possible obs: 59.6 % / Redundancy: 36.1 % / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.017 / Rrim(I) all: 0.1 / Rsym value: 0.13 / Net I/σ(I): 24 / Num. measured all: 715057 / Scaling rejects: 1 |
Reflection shell | Resolution: 1.642→1.86 Å / Redundancy: 34.8 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 1.6 / Num. measured all: 89508 / Num. unique obs: 2344 / CC1/2: 0.979 / Rpim(I) all: 0.143 / Rrim(I) all: 0.9 / Rsym value: 2.59 / Net I/σ(I) obs: 5.5 / % possible all: 9.8 |
-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: 1.642→56.678 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.29 / 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: 101.67 Å2 / Biso mean: 43.7054 Å2 / Biso min: 9.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.642→56.678 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 3.0635 Å / Origin y: 11.5786 Å / Origin z: -10.8889 Å
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Refinement TLS group |
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