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Open data
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Basic information
Entry | Database: PDB / ID: 1e8k | ||||||
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Title | Cyclophilin 3 Complexed With Dipeptide Ala-Pro | ||||||
![]() | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3 | ||||||
![]() | ISOMERASE | ||||||
Function / homology | ![]() cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, S.Y. / Dornan, J. / Kontopidis, G. / Taylor, P. / Walkinshaw, M.D. | ||||||
![]() | ![]() Title: The First Direct Determination of a Ligand Binding Constant in Protein Crystals Authors: Wu Sy, S.Y. / Dornan, J. / Kontopidis, G. / Taylor, P. / Walkinshaw, M.D. #1: ![]() Title: Biochemical and Structural Characterization Ivergent Loop Cyclophilin from Caenorhabditis Elegans of A Authors: Dornan, J. / Page, A.P. / Taylor, P. / Wu, S.Y. / Winter, A.D. / Husi, H. / Walkinshawr, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.9 KB | Display | ![]() |
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PDB format | ![]() | 36.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1dywS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18576.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ALA / |
#3: Chemical | ChemComp-PRO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 59.73 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: MPEG5000, SODIUM CITRATE, PH 5.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Dornan, J., (1999) J.Biol.Chem., 274, 34877. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 19230 / % possible obs: 97.6 % / Redundancy: 7.92 % / Rsym value: 0.079 / Net I/σ(I): 12.85 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.13 / Rsym value: 0.332 / % possible all: 88.2 |
Reflection | *PLUS Num. measured all: 152448 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Rmerge(I) obs: 0.332 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DYW Resolution: 1.9→10 Å / Num. parameters: 6247 / Num. restraintsaints: 5392 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1497.31 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.1826 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_bond_d / Dev ideal: 0.03 |