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- PDB-8b58: Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b58 | ||||||
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Title | Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with Cyclosporin A | ||||||
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Function / homology | ![]() protein peptidyl-prolyl isomerization / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Jimenez-Faraco, E. / Hermoso, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii . Authors: Favretto, F. / Jimenez-Faraco, E. / Conter, C. / Dominici, P. / Hermoso, J.A. / Astegno, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.5 KB | Display | ![]() |
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PDB format | ![]() | 158.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 22998.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | ![]() ![]() ![]() ![]() ![]() Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. Source: (synth.) synthetic construct (others) / References: ![]() #3: Water | ChemComp-HOH / | ![]() Compound details | CYCLOSPORI | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M citric acid pH 3.5, and 25% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.1→45.09 Å / Num. obs: 154928 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7984 / CC1/2: 0.71 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.304 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→45.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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