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Yorodumi- PDB-6r37: T. brucei FPPS in complex with 2-(5-chlorobenzo[b]thiophen-3-yl)a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r37 | ||||||
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Title | T. brucei FPPS in complex with 2-(5-chlorobenzo[b]thiophen-3-yl)acetic acid | ||||||
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 / Resolution: 2.1 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r37.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r37.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 6r37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r37 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r37 | HTTPS FTP |
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-Related structure data
Related structure data | 6r38C 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 BL21(DE3) (bacteria) / References: UniProt: Q86C09 |
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#2: Chemical | ChemComp-3N2 / ( |
#3: Chemical | ChemComp-DMS / |
-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: 43.17 % / Description: thin 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: 0.99996 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 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: 2.1→52.628 Å / Num. obs: 21086 / % possible obs: 91.3 % / Redundancy: 18.2 % / Biso Wilson estimate: 56.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.02 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.1→2.136 Å / Redundancy: 17.4 % / Rmerge(I) obs: 4.686 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1075 / CC1/2: 0.466 / Rpim(I) all: 1.135 / Rrim(I) all: 4.827 / Rsym value: 4.686 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ryp Resolution: 2.1→52.628 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.268 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.195
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Displacement parameters | Biso max: 219.29 Å2 / Biso mean: 92.83 Å2 / Biso min: 44.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→52.628 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 3.2875 Å / Origin y: 11.8605 Å / Origin z: -11.2889 Å
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Refinement TLS group | Selection details: { A|* } |