+Open data
-Basic information
Entry | Database: PDB / ID: 5kus | |||||||||||||||
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Title | Human cyclophilin A at 100K, Data set 6 | |||||||||||||||
Components | Peptidyl-prolyl cis-trans isomerase A | |||||||||||||||
Keywords | ISOMERASE / Conformational variation / Radiation damage | |||||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||
Authors | Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J Synchrotron Radiat / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kus.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kus.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kus_validation.pdf.gz | 410.9 KB | Display | wwPDB validaton report |
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Full document | 5kus_full_validation.pdf.gz | 411 KB | Display | |
Data in XML | 5kus_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 5kus_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5kus ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5kus | HTTPS FTP |
-Related structure data
Related structure data | 5kulC 5kunC 5kuoC 5kuqC 5kurC 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 (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å |
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→38.24 Å / Num. obs: 31585 / % possible obs: 93.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.041 / Rrim(I) all: 0.072 / Net I/σ(I): 10.7 / Num. measured all: 88054 / Scaling rejects: 44 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.957 / CC1/2: 0.309 / % possible all: 57.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F66 Resolution: 1.7→34.034 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.4 Å2 / Biso mean: 21.2644 Å2 / Biso min: 7.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→34.034 Å
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Refine LS restraints |
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LS refinement shell |
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