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- PDB-3eov: Crystal structure of cyclophilin from Leishmania donovani ligated... -
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Open data
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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 | ||||||
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![]() | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN | ||||||
Function / homology | ![]() peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Venugopal, V. / Dasgupta, D. / Datta, A.K. / Banerjee, R. | ||||||
![]() | ![]() 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: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 64.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.8 KB | Display | ![]() |
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Full document | ![]() | 458.1 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2haqS S: Starting model for refinement |
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Similar structure data |
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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: 19090.541 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.) ![]() #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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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