+Open data
-Basic information
Entry | Database: PDB / ID: 6u5d | |||||||||||||||
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Title | RT XFEL structure of CypA solved using LCP injection system | |||||||||||||||
Components | Peptidyl-prolyl cis-trans isomerase A | |||||||||||||||
Keywords | ISOMERASE / Peptidyl-prolyl / cis-trans / cyclophilin | |||||||||||||||
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 / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / 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 / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / 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 / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / 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 / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||||||||
Authors | Wolff, A.M. / Young, I.D. / Sierra, R.G. / Brewster, A.S. / Koralek, J.D. / Boutet, S. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Iucrj / Year: 2020 Title: Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals Authors: Wolff, A.M. / Young, I.D. / Sierra, R.G. / Brewster, A.S. / Martynowycz, M.W. / Nango, E. / Sugahara, M. / Nakane, T. / Ito, K. / Aquila, A. / Bhowmick, A. / Biel, J.T. / Carbajo, S. / ...Authors: Wolff, A.M. / Young, I.D. / Sierra, R.G. / Brewster, A.S. / Martynowycz, M.W. / Nango, E. / Sugahara, M. / Nakane, T. / Ito, K. / Aquila, A. / Bhowmick, A. / Biel, J.T. / Carbajo, S. / Cohen, A.E. / Cortez, S. / Gonzalez, A. / Hino, T. / Im, D. / Koralek, J.D. / Kubo, M. / Lazarou, T.S. / Nomura, T. / Owada, S. / Samelson, A. / Tanaka, T. / Tanaka, R. / Thompson, E.M. / van den Bedem, H. / Woldeyes, R.A. / Yumoto, F. / Zhao, W. / Tono, K. / Boutet, S. / Iwata, S. / Gonen, T. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u5d.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u5d.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 6u5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/6u5d ftp://data.pdbj.org/pub/pdb/validation_reports/u5/6u5d | HTTPS FTP |
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-Related structure data
Related structure data | 6u5cC 6u5eC 4yumS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1602169 / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.11577/1598261 / Data set type: diffraction image data |
Experimental dataset #3 | Data reference: 10.11577/1595660 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7.5 / Details: 100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.31 Å |
Detector | Type: RAYONIX MX170-HS / Detector: CCD / Date: Aug 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.31 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 25034 / % possible obs: 99.89 % / Redundancy: 98.9 % / Biso Wilson estimate: 19.85 Å2 / CC1/2: 0.945 / R split: 0.149 / Net I/σ(I): 4.062 |
Reflection shell | Resolution: 1.65→1.68 Å / Mean I/σ(I) obs: 1.076 / Num. unique obs: 1216 / CC1/2: 0.567 / R split: 0.543 |
Serial crystallography measurement | Pulse duration: 45 fsec. / XFEL pulse repetition rate: 10 Hz |
Serial crystallography sample delivery | Description: LCP (Weierstall et al., 2014) / Method: injection |
Serial crystallography data reduction | Frames indexed: 11821 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4YUM Resolution: 1.65→17.43 Å / SU ML: 0.1519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1489 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 26.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→17.43 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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