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Yorodumi- PDB-6r38: T. brucei FPPS in complex with 2-(2,5-dichlorobenzo[b]thiophen-3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r38 | ||||||
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Title | T. brucei FPPS in complex with 2-(2,5-dichlorobenzo[b]thiophen-3-yl)acetic acid | ||||||
Components | Farnesyl pyrophosphate synthase | ||||||
Keywords | TRANSFERASE / sterol biosynthesis / farnesyl diphosphate synthase / Trypanosoma brucei / homodimer | ||||||
Function / homology | Function and homology information farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å | ||||||
Authors | Muenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Thesis / Year: 2019 Title: Targeting Trypanosoma brucei FPPS by Fragment-based drug discovery Authors: Muenzker, L. / Wolfgang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r38.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r38.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 6r38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r38_validation.pdf.gz | 754.7 KB | Display | wwPDB validaton report |
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Full document | 6r38_full_validation.pdf.gz | 758.6 KB | Display | |
Data in XML | 6r38_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 6r38_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r38 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r38 | HTTPS FTP |
-Related structure data
Related structure data | 6r37C 4rypS S: Starting model for refinement C: citing same article (ref.) |
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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 Details: GP is an expression tag / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q86C09 |
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#2: Chemical | ChemComp-JQE / |
#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: 2.16 Å3/Da / Density % sol: 43.1 % |
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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: 0.99996 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99996 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→56.665 Å / Num. obs: 17098 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 50.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.328 / Rpim(I) all: 0.077 / Rrim(I) all: 0.337 / Rsym value: 0.328 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.33→2.37 Å / Redundancy: 19.8 % / Rmerge(I) obs: 11.166 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 812 / CC1/2: 0.458 / Rpim(I) all: 2.541 / Rrim(I) all: 11.456 / Rsym value: 11.166 / % possible all: 100 |
-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: 2.33→56.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.361 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.228
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Displacement parameters | Biso max: 185.75 Å2 / Biso mean: 84.44 Å2 / Biso min: 38.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→56.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 43
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Refinement TLS params. | Method: refined / Origin x: 3.3957 Å / Origin y: 11.8045 Å / Origin z: -11.3262 Å
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Refinement TLS group | Selection details: { A|* } |