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Yorodumi- PDB-5qpf: PanDDA analysis group deposition -- Crystal Structure of T. cruzi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qpf | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000478a | ||||||
Components | Farnesyl diphosphate synthase | ||||||
Keywords | TRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Petrick, J.K. / Nelson, E.R. / Muenzker, L. / Krojer, T. / Douangamath, A. / Brandao-Neto, J. / von Delft, F. / Dekker, C. / Jahnke, W. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition - FPPS screened against the DSI Fragment Library Authors: Petrick, J.K. / Muenzker, L. / von Delft, F. / Jahnke, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qpf.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qpf.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 5qpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/5qpf ftp://data.pdbj.org/pub/pdb/validation_reports/qp/5qpf | HTTPS FTP |
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-Group deposition
ID | G_1002063 (35 entries) |
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Title | PanDDA analysis group deposition - FPPS screened against the DSI Fragment Library |
Type | changed state |
Description | FPPS screened against the DSI Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 1yhkS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41359.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WS26 |
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-Non-polymers , 5 types, 338 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 80 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.5→98.82 Å / Num. obs: 65050 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 15.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.03 / Rrim(I) all: 0.126 / Net I/σ(I): 12.9 / Num. measured all: 1078620 / Scaling rejects: 1754 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1YHK Resolution: 1.5→49.744 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.04 / 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: 106.1 Å2 / Biso mean: 22.1799 Å2 / Biso min: 5.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→49.744 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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