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Yorodumi- PDB-3eov: Crystal structure of cyclophilin from Leishmania donovani ligated... -
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-Basic information
Entry | Database: PDB / ID: 3eov | ||||||
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Title | Crystal structure of cyclophilin from Leishmania donovani ligated with cyclosporin A | ||||||
Components |
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Keywords | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | LEISHMANIA DONOVANI (eukaryote) TOLYPOCLADIUM INFLATUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Venugopal, V. / Dasgupta, D. / Datta, A.K. / Banerjee, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of Cyclophilin from Leishmania Donovani Bound to Cyclosporin at 2.6 A Resolution: Correlation between Structure and Thermodynamic Data. Authors: Venugopal, V. / Datta, A.K. / Bhattacharyya, D. / Dasgupta, D. / Banerjee, R. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Structure of Cyclophilin from Leishmania Donovani at 1.97 A Resolution. Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R. #2: Journal: J.Biol.Chem. / Year: 2001 Title: Lack of Abundance of Cytoplasmic Cyclosporin A- Binding Protein Renders Free-Living Leishmania Donovani Resistant to Cyclosporin A. Authors: Dutta, M. / Delhi, P. / Sinha, K.M. / Banerjee, R. / Datta, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eov.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eov.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 3eov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eov_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 3eov_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 3eov_validation.xml.gz | 17 KB | Display | |
Data in CIF | 3eov_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/3eov ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eov | HTTPS FTP |
-Related structure data
Related structure data | 2haqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19090.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA DONOVANI (eukaryote) / Gene: CYP / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q9U9R3, 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.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A #3: Water | ChemComp-HOH / | Compound details | CYCLOSPORI | Sequence details | THE N-TERMINAL 5 RESIDUES 'HHHHHH' IN CHAINS A AND B IS AN ENGINEERED | |
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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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | pH: 8.5 Details: 0.02M TRIS, 15% PEG3350, 0.1M NACL, 0.02% AZIDE, PH 8.5, 6% ETHYL ALCOHOL, CONCENTRATION: 10 MG/ML 1:1 CYCLOPHILIN-CYCLOSPORIN COMPLEX, TEMPERATURE 292K, BATCH METHOD, PH 8.50, SMALL TUBES |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2008 / Details: OSMIC MAXFLUX CONFOCAL MULTILAY |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 12040 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 4.11 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.6 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HAQ Resolution: 2.6→27.48 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 780102.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.6 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→27.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.149 / Total num. of bins used: 6
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Xplor file |
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