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Yorodumi- PDB-8b58: Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii i... -
+Open data
-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 | ||||||
Components |
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Keywords | ISOMERASE / CYCLOPHILIN / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX | ||||||
Function / homology | Function and homology information protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å | ||||||
Authors | Jimenez-Faraco, E. / Hermoso, J.A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b58.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b58.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 8b58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b58_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 8b58_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 8b58_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 8b58_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/8b58 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/8b58 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_026260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6KAD1, peptidylprolyl isomerase #2: Protein/peptide | Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. Source: (synth.) synthetic construct (others) / References: Cyclosporin A #3: Water | ChemComp-HOH / | Compound details | CYCLOSPORI | 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: 2.13 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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å |
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: 0.97918 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.1→45.09 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.06 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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