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Yorodumi- PDB-6r08: T. cruzi FPPS in complex with 3-(carboxymethyl)-5,7-dichloro-1H-i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r08 | ||||||
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Title | T. cruzi FPPS in complex with 3-(carboxymethyl)-5,7-dichloro-1H-indole-2-carboxylic acid | ||||||
Components | Farnesyl diphosphate synthase | ||||||
Keywords | TRANSFERASE / farnesyl diphosphate synthase / sterol biosynthesis / farnesyl pyrophosphate / homodimer | ||||||
Function / homology | Function and homology information farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å | ||||||
Authors | Petrick, J.K. / Muenzker, L. / Schleberger, C. / Jahnke, W. | ||||||
Funding support | 1items
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Citation | Journal: Thesis / Year: 2019 Title: Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery Authors: Petrick, J.K. / Jahnke, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r08.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r08.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/6r08 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/6r08 | HTTPS FTP |
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-Related structure data
Related structure data | 6r04C 6r05C 6r06C 6r07C 6r09C 6r0aC 6r0bC 6r39C 6shvC 6si5C 4dwgS 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: 41359.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Termini not resolved / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WS26 | ||||
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#2: Chemical | ChemComp-GO1 / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #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: 2.33 Å3/Da / Density % sol: 47.19 % / Mosaicity: 0.06 ° |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 80 mM MES: 8.5 mM ZnSO4: 19.42 % PEG MME 550: 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 1.435→49.746 Å / Num. obs: 74408 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Rrim(I) all: 0.055 / Rsym value: 0.053 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.435→1.459 Å / Redundancy: 19.5 % / Rmerge(I) obs: 4.737 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3629 / CC1/2: 0.362 / Rpim(I) all: 1.094 / Rrim(I) all: 4.863 / Rsym value: 4.737 / % 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: 4DWG Resolution: 1.44→48.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.065
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Displacement parameters | Biso max: 110.25 Å2 / Biso mean: 35.92 Å2 / Biso min: 19.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.44→48.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: -8.8008 Å / Origin y: -17.3607 Å / Origin z: -20.4514 Å
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Refinement TLS group | Selection details: { A|* } |