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Open data
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Basic information
Entry | Database: PDB / ID: 3k0m | ||||||
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Title | Cryogenic structure of CypA | ||||||
![]() | Cyclophilin A | ||||||
![]() | ISOMERASE / proline isomerase / Cyclosporin / Host-virus interaction / Isopeptide bond / Phosphoprotein / Rotamase | ||||||
Function / homology | ![]() negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / integrin binding / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fraser, J.S. / Alber, T. | ||||||
![]() | ![]() Title: Hidden alternative structures of proline isomerase essential for catalysis. Authors: Fraser, J.S. / Clarkson, M.W. / Degnan, S.C. / Erion, R. / Kern, D. / Alber, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.9 KB | Display | ![]() |
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PDB format | ![]() | 90.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3k0nC ![]() 3k0oC ![]() 3k0pC ![]() 3k0qC ![]() 3k0rC ![]() 2cplS C: citing same article ( 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
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 22% PEG 3350, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2007 |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953695 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. all: 52646 / Num. obs: 54771 / % possible obs: 96.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.042 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 5385 / Rsym value: 0.564 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2cpl Resolution: 1.25→33.659 Å / SU ML: 0.11 / σ(F): 0.12 / Phase error: 12.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.403 Å2 / ksol: 0.435 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.25→33.659 Å
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Refine LS restraints |
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LS refinement shell |
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