+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yug | ||||||
---|---|---|---|---|---|---|---|
Title | Multiconformer synchrotron model of CypA at 100 K | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase A | ||||||
![]() | ISOMERASE / Cyclophilin | ||||||
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 | ![]() ![]() | ||||||
![]() | Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Hopkins, J.B. / Uervirojnangkoorn, M. ...Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Hopkins, J.B. / Uervirojnangkoorn, M. / McPhillips, S.E. / Song, J. / Mori, R.A. / Holton, J.M. / Weis, W.I. / Brunger, A.T. / Soltis, M. / Lemke, H. / Gonzalez, A. / Sauter, N.K. / Cohen, A.E. / van den Bedem, H. / Thorne, R.E. / Fraser, J.S. | ||||||
![]() | ![]() Title: Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Authors: Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Hopkins, J.B. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Uervirojnangkoorn, M. / McPhillips, S.E. ...Authors: Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Hopkins, J.B. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Uervirojnangkoorn, M. / McPhillips, S.E. / Song, J. / Alonso-Mori, R. / Holton, J.M. / Weis, W.I. / Brunger, A.T. / Soltis, S.M. / Lemke, H. / Gonzalez, A. / Sauter, N.K. / Cohen, A.E. / van den Bedem, H. / Thorne, R.E. / Fraser, J.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 140.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 114.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4yuhC ![]() 4yuiC ![]() 4yujC ![]() 4yukC ![]() 4yulC ![]() 4yumC ![]() 4yunC ![]() 4yuoC ![]() 4yupC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.04 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→38.085 Å / Num. obs: 32657 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.07 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 1.57 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.48→38.085 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 18.07 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→38.085 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|