+Open data
-Basic information
Entry | Database: PDB / ID: 6r36 | ||||||
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Title | T. brucei farnesyl pyrophosphate synthase (FPPS) | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE / sterol biosynthesis / farnesyl diphosphate synthase / Trypanosoma brucei / homodimer | ||||||
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: 1.67 Å | ||||||
Authors | Muenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Chembiochem / Year: 2020 Title: Fragment-Based Discovery of Non-bisphosphonate Binders of Trypanosoma brucei Farnesyl Pyrophosphate Synthase. Authors: Munzker, L. / Petrick, J.K. / Schleberger, C. / Clavel, D. / Cornaciu, I. / Wilcken, R. / Marquez, J.A. / Klebe, G. / Marzinzik, A. / Jahnke, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r36.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r36.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 6r36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r36 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r36 | HTTPS FTP |
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-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 Details: GP is an expression tag / 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-PEG / | #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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: needles |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.12 M Cesium chloride, 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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99974 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99974 Å / Relative weight: 1 |
Reflection | Resolution: 1.668→52.384 Å / Num. obs: 28487 / % possible obs: 63.8 % / Redundancy: 18.3 % / Biso Wilson estimate: 29.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Rsym value: 0.091 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.668→1.883 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.641 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1424 / CC1/2: 0.736 / Rpim(I) all: 0.437 / Rrim(I) all: 1.7 / Rsym value: 1.641 / % possible all: 10.7 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_TRA
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ryp Resolution: 1.67→27.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.144
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Displacement parameters | Biso max: 152.18 Å2 / Biso mean: 48.95 Å2 / Biso min: 12.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→27.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 2.6873 Å / Origin y: 11.9323 Å / Origin z: -11.1318 Å
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Refinement TLS group | Selection details: { A|* } |