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Open data
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Basic information
Entry | Database: PDB / ID: 5kul | |||||||||||||||
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Title | Human cyclophilin A at 100K, Data set 1 | |||||||||||||||
![]() | Peptidyl-prolyl cis-trans isomerase A | |||||||||||||||
![]() | ISOMERASE / Conformational variation / Radiation damage | |||||||||||||||
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 / leukocyte chemotaxis / endothelial cell activation / virion binding ...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 / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / 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 / Calcineurin activates NFAT / viral release from host cell / positive regulation of viral genome replication / Binding and entry of HIV virion / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin 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 / response to hypoxia / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational variation of proteins at room temperature is not dominated by radiation damage. Authors: Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.6 KB | Display | ![]() |
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Full document | ![]() | 422.5 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kunC ![]() 5kuoC ![]() 5kuqC ![]() 5kurC ![]() 5kusC ![]() 5kuuC ![]() 5kuvC ![]() 5kuwC ![]() 5kuzC ![]() 5kv0C ![]() 5kv1C ![]() 5kv2C ![]() 5kv3C ![]() 5kv4C ![]() 5kv5C ![]() 5kv6C ![]() 5kv7C ![]() 5kvwC ![]() 5kvxC ![]() 5kvzC ![]() 5kw0C ![]() 5kw3C ![]() 5kw4C ![]() 5kw5C ![]() 5kw7C ![]() 5kw8C ![]() 5kxkC ![]() 5kxlC ![]() 5kxmC ![]() 5kxnC ![]() 5kxoC ![]() 5kxpC ![]() 5kxrC ![]() 5kxsC ![]() 5kxtC ![]() 5kxwC ![]() 5kxxC ![]() 5kxyC ![]() 5kxzC ![]() 5ky1C ![]() 5f66S 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: 17905.307 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: 2.78 Å3/Da / Density % sol: 55.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→38.27 Å / Num. obs: 31534 / % possible obs: 93.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 13.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.038 / Rrim(I) all: 0.068 / Net I/σ(I): 13.1 / Num. measured all: 87886 / Scaling rejects: 60 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.525 / CC1/2: 0.704 / % possible all: 55.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F66 Resolution: 1.7→34.021 Å / FOM work R set: 0.8686 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.98 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.47 Å2 / Biso mean: 16.21 Å2 / Biso min: 2.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→34.021 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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